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SMART/DiffExpAnal/DESeqTools/HTseqClean.R SMART/DiffExpAnal/DESeqTools/MAplotDE.R SMART/DiffExpAnal/DESeqTools/RNAseqFunctions.R SMART/DiffExpAnal/DESeqTools/anadiffGenes2conds.R SMART/DiffExpAnal/DESeqTools/barplotNul.R SMART/DiffExpAnal/DESeqTools/barplotTC.R SMART/DiffExpAnal/DESeqTools/boxplotCounts.R SMART/DiffExpAnal/DESeqTools/clusterPlot.R SMART/DiffExpAnal/DESeqTools/densityPlot.R SMART/DiffExpAnal/DESeqTools/exportComplete.R SMART/DiffExpAnal/DESeqTools/exportDiff.R SMART/DiffExpAnal/DESeqTools/histoRawp.R SMART/DiffExpAnal/DESeqTools/loadCountData.R SMART/DiffExpAnal/DESeqTools/loadTargetFile.R SMART/DiffExpAnal/DESeqTools/majSequence.R SMART/DiffExpAnal/DESeqTools/pairwiseSERE.R SMART/DiffExpAnal/DESeqTools/pairwiseScatterPlots.R SMART/DiffExpAnal/DESeqTools/plotDispEstimates.R SMART/DiffExpAnal/DESeqTools/raw/f1cond1.tsv SMART/DiffExpAnal/DESeqTools/raw/f1cond2.tsv SMART/DiffExpAnal/DESeqTools/raw/f2cond1.tsv SMART/DiffExpAnal/DESeqTools/raw/f2cond2.tsv SMART/DiffExpAnal/DESeqTools/raw2counts.R SMART/DiffExpAnal/DESeqTools/removeNul.R SMART/DiffExpAnal/__init__.py SMART/DiffExpAnal/bam_to_sam_parallel.py SMART/DiffExpAnal/bam_to_sam_parallel.xml SMART/DiffExpAnal/bam_to_sam_parallel_unSQL.py SMART/DiffExpAnal/bam_to_sam_parallel_unSQL.xml SMART/DiffExpAnal/compareOverlapping_parallel.py SMART/DiffExpAnal/compareOverlapping_parallel.xml SMART/DiffExpAnal/compareOverlapping_parallel_unSQL.py SMART/DiffExpAnal/compareOverlapping_parallel_unSQL.xml SMART/DiffExpAnal/countNumber.pl SMART/DiffExpAnal/countNumber.xml SMART/DiffExpAnal/countNumber_parallel.py SMART/DiffExpAnal/countNumber_parallel.xml SMART/DiffExpAnal/countNumber_parallel_unSQL.py SMART/DiffExpAnal/countNumber_parallel_unSQL.xml SMART/DiffExpAnal/deseq.sh SMART/DiffExpAnal/deseq.xml SMART/DiffExpAnal/fastq_groomer_parallel.py SMART/DiffExpAnal/fastq_groomer_parallel.xml SMART/DiffExpAnal/fastq_groomer_parallel_unSQL.py SMART/DiffExpAnal/fastq_groomer_parallel_unSQL.xml SMART/DiffExpAnal/gsnap.xml SMART/DiffExpAnal/gsnap_parallel_unSQL.py SMART/DiffExpAnal/gsnap_parallel_unSQL.xml SMART/DiffExpAnal/listInputs.pl SMART/DiffExpAnal/listInputs.xml SMART/DiffExpAnal/loadHTSeqResultFiles.py SMART/DiffExpAnal/loadHTSeqResultFiles.xml SMART/DiffExpAnal/loadMultiFastqFiles.py SMART/DiffExpAnal/loadMultiFastqFiles.sh SMART/DiffExpAnal/loadMultiFastqFiles.xml SMART/DiffExpAnal/testR.R SMART/DiffExpAnal/testR.sh SMART/DiffExpAnal/tophat_parallel.py SMART/DiffExpAnal/tophat_parallel.xml SMART/DiffExpAnal/tophat_parallel_unSQL.py SMART/DiffExpAnal/tophat_parallel_unSQL.xml SMART/DiffExpAnal/wrappGSNAP.py SMART/bacteriaRegulatoryRegion_Detection/changeName.py SMART/bacteriaRegulatoryRegion_Detection/changeName.xml SMART/bacteriaRegulatoryRegion_Detection/colorGff.pl SMART/bacteriaRegulatoryRegion_Detection/colorGff.xml SMART/bacteriaRegulatoryRegion_Detection/coverageGff.pl SMART/bacteriaRegulatoryRegion_Detection/coverageGff.xml SMART/bacteriaRegulatoryRegion_Detection/interElementGff.pl SMART/bacteriaRegulatoryRegion_Detection/interElementGff.xml SMART/bacteriaRegulatoryRegion_Detection/listGff.sh SMART/bacteriaRegulatoryRegion_Detection/prepareAnnot.sh SMART/bacteriaRegulatoryRegion_Detection/prepareAnnot.xml SMART/bacteriaRegulatoryRegion_Detection/seedGff.pl SMART/bacteriaRegulatoryRegion_Detection/seedGff.xml SMART/bacteriaRegulatoryRegion_Detection/sortGff.pl SMART/bacteriaRegulatoryRegion_Detection/sortGff.xml SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.pl SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.xml SMART/bacteriaRegulatoryRegion_Detection/strictlyIncludeGff.pl SMART/bacteriaRegulatoryRegion_Detection/strictlyIncludeGff.xml SMART/bacteriaRegulatoryRegion_Detection/writeResToHTML.py SMART/bacteriaRegulatoryRegion_Detection/writeResToHTML.xml SMART/data/REF.fasta SMART/data/REF.fasta.fai SMART/data/SR1.fasta SMART/data/SR1.fastq SMART/data/SR2.fastq SMART/data/bamFile.bam SMART/data/dummy.fasta SMART/data/expRef.fasta SMART/data/expRef_withoutSplit.fasta SMART/data/output.png SMART/data/part0.bam SMART/data/part0.sam SMART/data/part1.bam SMART/data/part1.sam SMART/data/part2.bam SMART/data/part2.sam SMART/data/part3.bam SMART/data/part3.sam SMART/data/part4.bam SMART/data/part4.sam SMART/data/samFile.sam SMART/data/sortedBamFile.bam SMART/data/test.gff.gff3 SMART/data/test_clusterize.gff3 SMART/data/test_clusterize2.gff3 |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/HTseqClean.R --- a/SMART/DiffExpAnal/DESeqTools/HTseqClean.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,19 +0,0 @@ -# HTseqClean -# remove extra counts out of genes -# for HTseq output - -# input : rawCounts -# output : cleaned rawCounts - -# created Feb 6th, 2012 -# Modified Feb 16th, 2012 -# Marie-Agnes Dillies - - -HTseqClean <- function( rawCounts ){ - - row2remove <- c("alignment_not_unique", "ambiguous", "no_feature", "not_aligned", "too_low_aQual") - rawCounts <- rawCounts[!rawCounts$Id %in% row2remove,] - rawCounts[is.na(rawCounts)] <- 0 - return(rawCounts) -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/MAplotDE.R --- a/SMART/DiffExpAnal/DESeqTools/MAplotDE.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,16 +0,0 @@ -# MAplotDE -# MAplot of DE genes - -# input : res, alpha,OUT_MAplotDEName -# output : MAplot (png) - -MAplotDE <- function( res, alpha, OUT_MAplotDEName, out = TRUE ){ - - if (out) png( file=OUT_MAplotDEName ) - - plot( res$baseMean, res$log2FoldChange, pch=".", xlab="Mean expression", ylab="log2FC", main="", - log="x", col=ifelse(res$padj < alpha, "red", "black") ) - abline(h=0, col="red") - - if (out) dev.off() -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/RNAseqFunctions.R --- a/SMART/DiffExpAnal/DESeqTools/RNAseqFunctions.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,38 +0,0 @@ -# RNAseqFunctions -# when sourced, sources all R functions associated with RNAseq data analysis - -RNAseqFunctions <- function( RfuncDir ){ - - source(paste(RfuncDir, "loadTargetFile.R", sep="")) - source(paste(RfuncDir, "loadCountData.R", sep="")) -# source(paste(RfuncDir, "loadStrandData.R", sep="")) - source(paste(RfuncDir, "HTseqClean.R", sep="")) - source(paste(RfuncDir, "raw2counts.R", sep="")) - source(paste(RfuncDir, "barplotTC.R", sep="")) - source(paste(RfuncDir, "barplotNul.R", sep="")) - source(paste(RfuncDir, "removeNul.R", sep="")) - source(paste(RfuncDir, "densityPlot.R", sep="")) - source(paste(RfuncDir, "boxplotCounts.R", sep="")) - source(paste(RfuncDir, "majSequence.R", sep="")) - source(paste(RfuncDir, "clusterPlot.R", sep="")) - source(paste(RfuncDir, "pairwiseSERE.R", sep="")) - source(paste(RfuncDir, "pairwiseScatterPlots.R", sep="")) -# source(paste(RfuncDir, "pairwiseScatterPlotsAll.R", sep="")) - source(paste(RfuncDir, "plotDispEstimates.R", sep="")) -# source(paste(RfuncDir, "deseqByCond.R", sep="")) -# source(paste(RfuncDir, "edgeRByCond.R", sep="")) -# source(paste(RfuncDir, "fisher.R", sep="")) - source(paste(RfuncDir, "histoRawp.R", sep="")) -# source(paste(RfuncDir, "histoRawpMconds.R", sep="")) - source(paste(RfuncDir, "MAplotDE.R", sep="")) -# source(paste(RfuncDir, "MAplotDEMconds.R", sep="")) - source(paste(RfuncDir, "exportComplete.R", sep="")) -# source(paste(RfuncDir, "exportCompleteEdgeR.R", sep="")) -# source(paste(RfuncDir, "exportCompleteFisher.R", sep="")) -# source(paste(RfuncDir, "exportCompleteMconds.R", sep="")) -# source(paste(RfuncDir, "exportCompleteByCond.R", sep="")) -# source(paste(RfuncDir, "exportCompletePaired.R", sep="")) - source(paste(RfuncDir, "exportDiff.R", sep="")) -# source(paste(RfuncDir, "synthese.R", sep="")) -# source(paste(RfuncDir, "exportDiffByCond.R", sep="")) -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/anadiffGenes2conds.R --- a/SMART/DiffExpAnal/DESeqTools/anadiffGenes2conds.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,191 +0,0 @@ -# Analyse differentielle de donnees d expression par gene -# avec DESeq -# 2 conditions - -args <- commandArgs() -#print(args[1]) -#print(args[2]) -#print(args[3]) -#print(args[4]) -#print(args[5]) -#print(args[6]) -#output file names -#print(args[7]) # HTML file name -#print(args[8]) # HTML file all images directory -#print(args[9]) # complete xls file name -#print(args[10])# UP xls file name -#print(args[11]) #Down xls file name -#print(args[12]) #the executable scipt (for getting the path) - -library(R2HTML) -library(R.utils) - -#run example: -projectName <- "DESeqAnalysis" -analysisVersion <- "V1" # fitType=local, sharingMode=fit-only, method=blind -rawDir <- "raw" -targetFile <- args[4] -header <- as.integer(args[5]) #si on a header ou pas, si on a, header=1, sinon header=0 -withOutReplicates <- as.integer(args[6]) - -#get the directory to write the results -tab <- splitByPattern(args[7], pattern="/") -res_dir <- "" -for (e in tab[1:length(tab)-1]) { res_dir <- paste(res_dir, e, sep="")} -#get the html output file name -OUT_HTMLname <- args[7] -#get the images directory to write to -OUT_imgDir <- args[8] -#if the directory dosen't existe, we should create it first - -alpha <- 0.05 -adjMethod <- "BH" -outfile <- T -runningScriptTab <- splitByPattern(args[12], pattern="/") -RfuncDir <- "" -for (r in runningScriptTab[1:length(runningScriptTab)-1]) { RfuncDir <- paste(RfuncDir, r, sep="")} #find the path of executable script -RfuncDir <- paste(RfuncDir, "DESeqTools/", sep="") #define the function files path -# Dossier contenant les fonctions -print(RfuncDir) -source( paste(RfuncDir, "RNAseqFunctions.R", sep="/") ) - -# Chargement des packages et des fonctions -library(DESeq) -RNAseqFunctions(RfuncDir) -# Chargement du target file -target <- loadTargetFile( targetFile, header ) -# Chargement des donnees, construction d'une table de comptages par gene -#have changed -rawCounts <- loadCountData( target, header ) -conds <- unique(target$group) -cond1 <- as.character(conds[1]) -cond2 <- as.character(conds[!conds == conds[1]]) -rawCounts <- HTseqClean( rawCounts ) - -# Transformation en matrice de comptages -counts <- raw2counts( rawCounts )[[1]] - -# Nombre de reads par echantillon -OUT_barplotTCName <- paste(OUT_imgDir, "barplotTC.png", sep="/") -barplotTC( counts, target$group, OUT_barplotTCName, out=outfile ) - -# Proportion comptages nuls -OUT_barplotNulName <- paste(OUT_imgDir, "barplotNul.png", sep="/") -barplotNul( counts, target$group, OUT_barplotNulName, out=outfile ) - -# Suppression comptages nuls -counts <- removeNul( counts )[[1]] - -# Density plot -OUT_densityPlotName <- paste(OUT_imgDir, "densityPlot.png", sep="/") -densityPlot( counts, target$group, OUT_densityPlotName, out=outfile ) - -# Boxplot -OUT_boxplotCountsName <- paste(OUT_imgDir, "boxplotCounts.png", sep="/") -boxplotCounts( counts, target$group, type = c("raw", "norm"), OUT_boxplotCountsName, out=outfile ) -# Sequence majoritaire -OUT_majSequenceName <- paste(OUT_imgDir, "majSequence.png", sep="/") -majSequence( counts, target$group, OUT_majSequenceName, out=outfile ) - -# ScatterPlot between two samples -OUT_scatterPlot <- paste(OUT_imgDir, "scatterPlot.png", sep="/") -pairwiseScatterPlots(counts, target, OUT_scatterPlot, out=outfile, pdffile=FALSE) - -# SERE coefficient calculation (Poisson hypothesis for replicates techiques), to know if the variability between the réplicates or the conditons is hight or not. -coef <- pairwiseSERE(counts) -print(coef) -coef -# Creation structure de donnees cds, !! we use newCountDataset because that we have first column not numeric, and DESeq dosen't take non numeric values. -cds <- newCountDataSet( counts, target$group ) - -# Diagnostic for clustering of non-normalized samples -OUT_clusterPlot_before <- paste(OUT_imgDir, "clusteringOfSamplesBefore.png", sep="/") -clusterPlot(cds, OUT_clusterPlot_before, out=outfile) - - -# Normalisation (calcul des lib size factors ) -cds <- estimateSizeFactors( cds ) - -# Estimation de la dispersion -# parametres: - # method: how samples are pooled to estimate dispersion. If no replicates use "blind" - # sharingMode: how variance estimate is computed with respect to the fitted line. - # "Maximum" is the most conservative (max between fit and estimation), "fit-only" keeps the estimated value - # fitType: refers to the model. "Local" is the published model, "parametric" is glm-based (may not converge), now we use "parametric" as default value. -#in this case, without replicates -if(withOutReplicates!=0){ - cds <- estimateDispersions( cds, sharingMode="fit-only", method="blind") -} else if(withOutReplicates==0){ - #cds <- estimateDispersions( cds, sharingMode="fit-only", fitType="local")} - cds <- estimateDispersions( cds)} -# Analyse differentielle, ajustement BH par defaut -res <- nbinomTest( cds, cond1, cond2) - -# Diagnostic for clustering of normalized samples -OUT_clusterPlot <- paste(OUT_imgDir, "clusteringOfSamples.png", sep="/") -clusterPlot(cds, OUT_clusterPlot, out=outfile) - -# Control plot of dispersion estimates -OUT_plotDispEstimatesName <- paste(OUT_imgDir, "disperssionEstimates.png", sep="/") -plotDispEstimates( cds, OUT_plotDispEstimatesName, out=outfile ) - -# Distribution of raw p-values -OUT_histoRawpName <- paste(OUT_imgDir, "histoRawPvalue.png", sep="/") -histoRawp( res, OUT_histoRawpName, out=outfile ) - -# MAplot showing DE genes -OUT_MAplotDEName <- paste(OUT_imgDir, "MAplotDE.png", sep="/") -MAplotDE( res, alpha, OUT_MAplotDEName, out=outfile ) - -# export complete data -OUT_completeName <- args[9] -complete <- exportComplete( counts, res, target, adjMethod, cond1, cond2, OUT_completeName, out=outfile ) - -# export significant genes -OUT_upName <- args[10] -OUT_downName <- args[11] -diff <- exportDiff( complete, alpha, adjMethod, OUT_upName, OUT_downName, out=outfile ) - -# write all images results into an HTML file -prefixHTMLname <- tab[length(tab)] -#HTMLCSS(file.path(res_dir), filename=prefixHTMLname, CSSfile="R2HTML") -HTMLInitFile(file.path(res_dir), filename=prefixHTMLname, BackGroundColor="white") -HTML.title("<center>Differential Expression DESeq analysis.", HR=1) -HTML.title("<center>BarplotTC: number of RNA-seq reads per sample.", HR=2) - HTMLInsertGraph("barplotTC.png") - -HTML.title("<center>BarplotNul: number of RNA-seq reads that the count is 0 (nul).", HR=2) - HTMLInsertGraph("barplotNul.png") - -HTML.title("<center>DensityPlot: density of each sample.", HR=2) - HTMLInsertGraph("densityPlot.png") - -HTML.title("<center>Boxplot: number of RNA-seq reads distribution per sample.", HR=2) - HTMLInsertGraph("boxplotCounts.png") - -HTML.title("<center>MajorSequence: the proportion of reads associated with the most expressed sequence.", HR=2) - HTMLInsertGraph("majSequence.png") - -HTML.title("<center>ScatterPlot: Scatter plot of samples.", HR=2) - HTMLInsertGraph("scatterPlot.png") - -HTML.title("<center>Clustering Of No-Normalized Samples: Representing the no-normalized samples in Diagnostic.", HR=2) - HTMLInsertGraph("clusteringOfSamplesBefore.png") - -HTML.title("<center>Clustering Of Normalized Samples: Representing the normalized samples in Diagnostic.", HR=2) - HTMLInsertGraph("clusteringOfSamples.png") - -HTML.title("<center>DispersionEstimates: representing dispersion estimates vs mean expression.", HR=2) - HTMLInsertGraph("disperssionEstimates.png") - -HTML.title("<center>HistoRawPValue: histogram of raw p-value.", HR=2) - HTMLInsertGraph("histoRawPvalue.png") - -HTML.title("<center>MAplotDE: the differentially expressed genes (red point).", HR=2) - HTMLInsertGraph("MAplotDE.png") -HTMLEndFile() -absoluPrefixHTMLname <- paste(res_dir, prefixHTMLname, sep="") -outName <- paste(absoluPrefixHTMLname, ".html", sep="") -# change name is to be adapted into Galaxy -file.rename(outName, OUT_HTMLname) - |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/barplotNul.R --- a/SMART/DiffExpAnal/DESeqTools/barplotNul.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,19 +0,0 @@ -# barplotNul -# barplot representing null counts per sample - -# input : counts, target, projectName -# output : barplotNul (png) - -# created Feb 7th, 2012 -# modified April 30th, 2012 (target$group instead of target) - -barplotNul <- function( counts, group, OUT_barplotNulName, out = TRUE ){ - - if (out) png( file=OUT_barplotNulName ) - - N <- apply(counts, 2, function(x){sum(x == 0)})/nrow(counts) - barplot(N, col=as.integer(group)+1, main = "Proportion of null counts per Sample", ylim = c(0,1)) - legend("topright", as.character(unique(group)), lty=1, col=as.integer(unique(group))+1) - - if (out) dev.off() -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/barplotTC.R --- a/SMART/DiffExpAnal/DESeqTools/barplotTC.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,20 +0,0 @@ -# barplotTC -# barplot representing total count per sample - -# input : counts, target, projectName -# output : barplotTC (png) - -# created Feb 7th, 2012 -# modified April 30th, 2012 (group instead of target$group) - -barplotTC <- function( counts, group, OUT_barplotTCName, out = TRUE ){ - - if (out) png( file=OUT_barplotTCName ) - - ylim <- c(0, max(colSums(counts))*1.2) - barplot( colSums(counts), col=as.integer(group)+1, main = "Total Read Count per Sample", ylim=ylim ) - legend( "topright", as.character(unique(group)), lty=1, - col=as.integer(unique(group))+1 ) - - if (out) dev.off() -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/boxplotCounts.R --- a/SMART/DiffExpAnal/DESeqTools/boxplotCounts.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,18 +0,0 @@ -# boxplotCounts -# boxplots representing counts distribution per sample - -# input : counts, target, projectName, type of data (raw or norm) -# output : boxplot (png) - -# created Feb 7th, 2012 -# modified April 30th, 2012 - -boxplotCounts <- function( counts, group, type = c("raw", "norm"), OUT_boxplotCountsName, out = TRUE ){ - - if (out) png( file=OUT_boxplotCountsName ) - - boxplot( log2(counts+1), col=as.integer(group)+1, main = paste(type[1], " counts distribution", sep="" ) ) - legend( "topright", as.character(unique(group)), lty=1, col=as.integer(unique(group))+1 ) - - if (out) dev.off() -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/clusterPlot.R --- a/SMART/DiffExpAnal/DESeqTools/clusterPlot.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,27 +0,0 @@ -# clusterPlot -# dendrogram of sample clustering - -# input : counts, outputName, type of data (raw or norm) -# output : dendrogram (jpeg) - -# created Sept 13th, 2012 -# modified Oct 30th, 2012 -# Marie-Agnes Dillies - - -clusterPlot <- function( cds, OUT_clusterPlot, type = "raw", out = TRUE ){ - - if (out) png( file=OUT_clusterPlot ) - - if (type == "norm"){ - cdsblind <- estimateDispersions( cds, method="blind" ) - vsd <- getVarianceStabilizedData( cdsblind ) - } - else { - vsd <- counts(cds) - } - hc <- hclust( dist(t(vsd)), method="ward" ) - plot( hc, xlab = "Euclidean distance, Ward criterion", main=paste("Cluster Dendrogram, ", type, " data", sep="") ) - - if (out) dev.off() -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/densityPlot.R --- a/SMART/DiffExpAnal/DESeqTools/densityPlot.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,23 +0,0 @@ -# densityPlot -# density plot of all samples - -# input : counts, target, projectName -# output : densplot (png) - -# created Feb 7th, 2012 -# modified April 30th, 2012 - - -densityPlot <- function( counts, group, OUT_densityPlotName, out = TRUE ){ - - if (out) png( file=OUT_densityPlotName ) - - couleurs <- as.integer( group ) + 1 - ylim <- c(0, max(density(log2(counts)+1)$y)*1.5) - plot( density(log2(counts[,1])+1), main="Density of counts distribution", col=couleurs[1], ylim = ylim ) - for (i in 2:ncol(counts)) - lines( density(log2(counts[,i])+1), col=couleurs[i] ) - legend( "topright", as.character(unique(group)), lty=1, col=as.integer(unique(group))+1 ) - - if (out) dev.off() -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/exportComplete.R --- a/SMART/DiffExpAnal/DESeqTools/exportComplete.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,20 +0,0 @@ -# exportComplete -# export complete data and results - -# input : counts res, target -# output : complete data and xls file (in text format) - -# created Feb 14th, 2012 -# modified March 9th, 2012 (order of cond1 and cond2) - - -exportComplete <- function( counts, res, target, adjMethod, cond1, cond2, OUT_completeName, out = T ){ - - complete <- data.frame( res$id, counts, res[,3:ncol(res)] ) - colnames(complete) <- c( "id", as.character(target$label), cond2, cond1, "FC", "log2FC", "rawp", - paste("adjp",adjMethod,sep="") ) - - if (out) - write.table( complete, file=OUT_completeName, sep="\t", row.names=F ) - return( complete ) -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/exportDiff.R --- a/SMART/DiffExpAnal/DESeqTools/exportDiff.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,42 +0,0 @@ -# exportDiff -# export differentially expressed genes - -# input : complete, alpha, adjMethod, projectName -# output : diff genes, up and down in xls files - -# created Feb 14th, 2012 - - -exportDiff <- function( complete, alpha, adjMethod, OUT_upName, OUT_downName, out = T ){ - - diff <- complete[which(complete[,grep("adjp",colnames(complete))] < alpha),] - - gup <- up( diff ) - gdown <- down( diff ) - - if (out){ - gup[,(ncol(gup)-4):ncol(gup)] <- format( gup[,(ncol(gup)-4):ncol(gup)], digits=3, dec=",") - gdown[,(ncol(gdown)-4):ncol(gdown)] <- format( gdown[,(ncol(gdown)-4):ncol(gdown)], digits=3, dec=",") - write.table(gup, file=OUT_upName, row.names=F, sep="\t") - write.table(gdown, file=OUT_downName, row.names=F, sep="\t") - } - return( diff ) -} - - -up <- function( diff ){ - - up <- diff[diff$log2FC > 0,] - up <- up[order(up[,grep("adjp",colnames(up))]),] - - return( up ) -} - - -down <- function( diff ){ - - down <- diff[diff$log2FC < 0,] - down <- down[order(down[,grep("adjp",colnames(down))]),] - - return( down ) -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/histoRawp.R --- a/SMART/DiffExpAnal/DESeqTools/histoRawp.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,18 +0,0 @@ -# histoRawp -# histogram of raw p-values - -# input : res, OUT_histoRawpName -# output : histogram (png) - - -histoRawp <- function( res, OUT_histoRawpName, out = TRUE ){ - - if (out) png( file=OUT_histoRawpName ) - - ind <- grep("val", colnames(res)) - hist( res[,ind], nclass=50, xlab="Raw p-values", main="", col="skyblue" ) - - if (out) dev.off() -} - - |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/loadCountData.R --- a/SMART/DiffExpAnal/DESeqTools/loadCountData.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,36 +0,0 @@ -# loadCountData -# loads counts, one file per lane -# file names from target file - -# input : target -# output : raw count table - -# created Feb 6th, 2012 -# modified May 2nd, 2012 (colnames -> target$label) -# Marie-Agnes Dillies - - -loadCountData <- function(target, header){ - - require(DESeq) - fileNames <- target$files - -if(header!=0){ - #rawCounts <- read.table(as.character(paste(rawDir,target$files[1],sep="/")), sep="\t", header=TRUE) - rawCounts <- read.table(as.character(target$files[1],sep="/"), sep="\t", header=TRUE) -} else if(header==0){ - rawCounts <- read.table(as.character(target$files[1],sep="/"), sep="\t")} - - colnames(rawCounts) <- c("Id", as.character(target$label[1])) - - for (i in 2:length(fileNames)){ - if(header!=0){ - tmp <- read.table(as.character(target$files[i],sep="/"), sep="\t", header=TRUE) - } else if(header==0){ - tmp <- read.table(as.character(target$files[i],sep="/"), sep="\t")} - colnames(tmp) <- c("Id", as.character(target$label[i])) - rawCounts <- merge(rawCounts, tmp, by="Id", all=T) - } - rawCounts[is.na(rawCounts)] <- 0 - return(rawCounts) -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/loadTargetFile.R --- a/SMART/DiffExpAnal/DESeqTools/loadTargetFile.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,17 +0,0 @@ -# loadTargetFile -# loads file containing sample info - -# input : targetFile Name -# output : target - -# created Feb 6th, 2012 -# Marie-Agnes Dillies - - -loadTargetFile <- function(targetFile, header){ -if(header!=0){ - return(read.table(targetFile, header=T, sep="\t")) - }else if(header==0){ - return(read.table(targetFile, sep="\t")) - } -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/majSequence.R --- a/SMART/DiffExpAnal/DESeqTools/majSequence.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,26 +0,0 @@ -# majSequence -# compute proportion of reads associated with most expressed sequence - -# input : counts, target, projectName -# output : barplot, % associated with majority gene - -# created Feb 7th, 2012 -# modified Feb 20th, 2012 -# modified April 30th, 2012 -# Marie-Agnes Dillies - - -majSequence <- function( counts, group, OUT_majSequenceName, out = T, position = "topright" ){ - - if (out) png( file=OUT_majSequenceName ) - - maj <- apply(counts, 2, function(x){x <- x[order(x, decreasing=T)]; x[1]*100/sum(x)}) - seqname <- apply(counts, 2, function(x){x <- x[order(x, decreasing=T)]; names(x)[1]}) - - x <- barplot( maj, col=as.integer(group)+1, main = "Proportion of reads from most expressed gene", - ylim = c(0, max(maj)*1.2), cex.main=0.8 ) - for (i in 1:length(seqname)) text( x[i], maj[i]/2, seqname[i], cex=0.8, srt=90, adj=0) - legend( position, as.character(unique(group)), lty=1, col=as.integer(unique(group))+1 ) - - if (out) dev.off() -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/pairwiseSERE.R --- a/SMART/DiffExpAnal/DESeqTools/pairwiseSERE.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,41 +0,0 @@ -# pairwiseSERE -# compute pairwise SERE statistics - -# input : counts -# output : matrix of SERE values - -# created october 19th, 2012 -# Marie-Agnes Dillies - - -pairwiseSERE <- function( counts ){ - - sere <- matrix( NA, ncol=ncol(counts), nrow=ncol(counts) ) - for (i in 1:ncol(counts)){ - for (j in 1:ncol(counts)){ - sere[i,j] <- sigfun_Pearson( counts[,c(i,j)] ) - } - } - colnames(sere) <- rownames(sere) <- colnames(counts) - return( formatC(sere, format="f", digits=2) ) -} - -sigfun_Pearson <- function(observed) { - #calculate lambda and expected values - laneTotals<- colSums(observed); - total <- sum(laneTotals) - fullObserved <- observed[rowSums(observed)>0,]; - fullLambda <- rowSums(fullObserved)/total; - fullLhat <- fullLambda > 0; - fullExpected<- outer(fullLambda, laneTotals); - - #keep values - fullKeep <- which(fullExpected > 0); - - #calculate degrees of freedom (nrow*(ncol -1) >> number of parameters - calculated (just lamda is calculated >> thats why minus 1) - #calculate pearson and deviance for all values - oeFull <- (fullObserved[fullKeep] - fullExpected[fullKeep])^2/ fullExpected[fullKeep] # pearson chisq test - dfFull <- length(fullKeep) - sum(fullLhat!=0); - - return(c(sqrt(sum(oeFull)/dfFull))); -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/pairwiseScatterPlots.R --- a/SMART/DiffExpAnal/DESeqTools/pairwiseScatterPlots.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,31 +0,0 @@ -# pairwiseScatterPlots -# scatter plots for pairwise comparaisons of log counts - -# input : counts, target, outputName -# output : scatter plots (pdf: allows multiple figures in one file) - -# created Feb 21th, 2012 -# modified Sept 27th, 2012 (pdf output file) -# modified Oct 30th, 2012 (png) -# Marie-Agnes Dillies - - -pairwiseScatterPlots <- function( counts, target, OUT_scatterPlot, out = TRUE, pdffile = FALSE ){ - - if (out & !pdffile) png( OUT_scatterPlot ) - if (pdffile) pdf( OUT_scatterPlot ) - - conds <- unique(target$group) - # colnames(counts) <- target$label - - for (i in 1:(length(conds)-1)){ - for (j in (i+1):length(conds)){ - cond1 <- conds[i]; cond2 <- conds[j] - pairs( log2(counts[, which(target$group %in% c(as.character(cond1), as.character(cond2)))]+1), - pch=".", cex=0.5, main = paste(cond1, cond2, sep=" vs ") ) - } - } - - if (pdffile) dev.off() - if (out) dev.off() -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/plotDispEstimates.R --- a/SMART/DiffExpAnal/DESeqTools/plotDispEstimates.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,21 +0,0 @@ -# plotDispEstimates -# scatter plots representing dispersion estimates vs mean expression - -# input : cds, OUT_plotDispEstimatesName -# output : scatterplot (png) - -plotDispEstimates <- function( cds, OUT_plotDispEstimatesName, out = TRUE ){ - - if (out) png( file=OUT_plotDispEstimatesName ) - - plot( - rowMeans( counts(cds, normalized=T) ), - fitInfo(cds)$perGeneDispEsts, - pch=".", log="xy", - xlab = "Mean expression strength", ylab = "Dispersion estimate" ) - - xg <- 10^seq(-.5, 5, length.out=300) - lines( xg, fitInfo(cds)$dispFun(xg), col="red" ) - - if (out) dev.off() -} |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/raw/f1cond1.tsv --- a/SMART/DiffExpAnal/DESeqTools/raw/f1cond1.tsv Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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|
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/raw/f1cond2.tsv --- a/SMART/DiffExpAnal/DESeqTools/raw/f1cond2.tsv Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,18761 +0,0 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|
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/raw/f2cond1.tsv --- a/SMART/DiffExpAnal/DESeqTools/raw/f2cond1.tsv Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,18761 +0,0 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|
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/raw/f2cond2.tsv --- a/SMART/DiffExpAnal/DESeqTools/raw/f2cond2.tsv Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,18761 +0,0 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|
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/raw2counts.R --- a/SMART/DiffExpAnal/DESeqTools/raw2counts.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,20 +0,0 @@ -# raw2counts -# extract counts only from rawCounts -# and add rownames to counts - -# input : rawCounts -# output : counts - -# created Feb 6th, 2012 -# modified April 12, 2012 -# Marie-Agnes Dillies - - -raw2counts <- function( rawCounts, annot=1 ){ - - ex <- 1:annot - counts <- as.matrix( rawCounts[,-ex] ) - rownames(counts) <- rawCounts[,1] - infoCounts <- rawCounts[,ex] - return( list("counts"=counts, "infoCounts"= infoCounts) ) -} |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/DESeqTools/removeNul.R --- a/SMART/DiffExpAnal/DESeqTools/removeNul.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,14 +0,0 @@ -# removeNul -# remove genes with null counts in all samples - -# input : counts -# output : counts - -# created Feb 7th, 2012 -# Marie-Agnes Dillies - - -removeNul <- function( counts, info = NULL ){ - - return( list(counts[rowSums(counts) > 0,], info[rowSums(counts) > 0,]) ) -} |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/bam_to_sam_parallel.py --- a/SMART/DiffExpAnal/bam_to_sam_parallel.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,172 +0,0 @@ -#!/usr/bin/env python -""" -Converts BAM data to sorted SAM data. -usage: bam_to_sam.py [options] - --input1: SAM file to be converted - --output1: output dataset in bam format -""" - -import optparse, os, sys, subprocess, tempfile, shutil, tarfile, random -#from galaxy import eggs -#import pkg_resources; pkg_resources.require( "bx-python" ) -#from bx.cookbook import doc_optparse -#from galaxy import util - -def stop_err( msg ): - sys.stderr.write( '%s\n' % msg ) - sys.exit() - -def toTar(tarFileName, samOutputNames): - dir = os.path.dirname(tarFileName) - tfile = tarfile.open(tarFileName + ".tmp.tar", "w") - currentPath = os.getcwd() - os.chdir(dir) - for file in samOutputNames: - relativeFileName = os.path.basename(file) - tfile.add(relativeFileName) - os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName)) - tfile.close() - os.chdir(currentPath) - - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option('-t', '--tar', dest='outputTar', default=None, help='output all SAM results in a tar file.' ) - parser.add_option( '', '--input1', dest='input1', help='The input list of BAM datasets on txt format.' ) - #parser.add_option( '', '--input1', dest='input1', help='The input BAM dataset' ) - parser.add_option( '', '--output1', dest='output1', help='The output list of SAM datasets on txt format.' ) - #parser.add_option( '', '--output1', dest='output1', help='The output SAM dataset' ) - parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) - ( options, args ) = parser.parse_args() - - - #Parse the input txt file and read a list of BAM files. - file = open(options.input1, "r") - lines = file.readlines() - inputFileNames = [] - samOutputNames = [] - outputName = options.output1 - resDirName = os.path.dirname(outputName) + '/' - #Write output txt file and define all output sam file names. - out = open(outputName, "w") - for line in lines: - tab = line.split() - inputFileNames.append(tab[1]) - samOutName = resDirName + tab[0] + '_samOutput_%s.sam' % random.randrange(0, 10000) - samOutputNames.append(samOutName) - out.write(tab[0] + '\t' + samOutName + '\n') - file.close() - out.close() - - # output version # of tool - try: - tmp_files = [] - tmp = tempfile.NamedTemporaryFile().name - tmp_files.append(tmp) - tmp_stdout = open( tmp, 'wb' ) - proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout ) - tmp_stdout.close() - returncode = proc.wait() - stdout = None - for line in open( tmp_stdout.name, 'rb' ): - if line.lower().find( 'version' ) >= 0: - stdout = line.strip() - break - if stdout: - sys.stdout.write( 'Samtools %s\n' % stdout ) - else: - raise Exception - except: - sys.stdout.write( 'Could not determine Samtools version\n' ) - - - - tmp_dirs = [] - for i in range(len(inputFileNames)): - try: - # exit if input file empty - if os.path.getsize( inputFileNames[i] ) == 0: - raise Exception, 'Initial input txt file is empty.' - # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command - # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted - # into memory ( controlled by option -m ). - tmp_dir = tempfile.mkdtemp() - tmp_dirs.append(tmp_dir) - tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir ) - tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name - tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name - tmp_files.append(tmp_sorted_aligns_file_name) - tmp_sorted_aligns_file.close() - - command = 'samtools sort %s %s' % ( inputFileNames[i], tmp_sorted_aligns_file_base ) - tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - # exit if sorted BAM file empty - if os.path.getsize( tmp_sorted_aligns_file_name) == 0: - raise Exception, 'Intermediate sorted BAM file empty' - except Exception, e: - stop_err( 'Error sorting alignments from (%s), %s' % ( inputFileNames[i], str( e ) ) ) - - try: - # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). - if options.header: - view_options = "-h" - else: - view_options = "" - command = 'samtools view %s -o %s %s' % ( view_options, samOutputNames[i], tmp_sorted_aligns_file_name ) - tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - except Exception, e: - stop_err( 'Error extracting alignments from (%s), %s' % ( inputFileNames[i], str( e ) ) ) - if os.path.getsize( samOutputNames[i] ) > 0: - sys.stdout.write( 'BAM file converted to SAM' ) - else: - stop_err( 'The output file is empty, there may be an error with your input file.' ) - - if options.outputTar != None: - toTar(options.outputTar, samOutputNames) - #clean up temp files - for tmp_dir in tmp_dirs: - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - #print tmp_files - #for tmp in tmp_files: - # os.remove(tmp) - - -if __name__=="__main__": __main__() |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/bam_to_sam_parallel.xml --- a/SMART/DiffExpAnal/bam_to_sam_parallel.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,32 +0,0 @@ -<tool id="bam_to_sam_parallel" name="BAM to SAM (for DEA)" version="1.0.0"> - <description>converts a list of BAM format files to SAM format.</description> - <requirements> - <requirement type="package">samtools</requirement> - </requirements> - <command interpreter="python"> bam_to_sam_parallel.py - --input1=$input1 - --output1=$output1 - $header - $tar $outputTarFile - </command> - <inputs> - <param name="input1" type="data" format="txt" label="BAM File LIST to Convert" /> - <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /> - <param name="tar" type="boolean" truevalue="-t" falsevalue="" checked="false" label="tar option" help="This option creates a tar file for all out results." /> - </inputs> - <outputs> - <data format="txt" name="output1" label="converted SAM LIST files " /> - <data name="outputTarFile" format="tar"> - <filter>tar</filter> - </data> - </outputs> - <help> - -**What it does** - -This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. - -.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml - - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/bam_to_sam_parallel_unSQL.py --- a/SMART/DiffExpAnal/bam_to_sam_parallel_unSQL.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,145 +0,0 @@ -#!/usr/bin/env python -""" -Converts BAM data to sorted SAM data. -usage: bam_to_sam.py [options] - --input1: SAM file to be converted - --output1: output dataset in bam format -""" - -import optparse, os, sys, subprocess, tempfile, shutil, tarfile, random -from commons.core.launcher.Launcher import Launcher -from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory -#from galaxy import eggs -#import pkg_resources; pkg_resources.require( "bx-python" ) -#from bx.cookbook import doc_optparse -#from galaxy import util - -def stop_err( msg ): - sys.stderr.write( '%s\n' % msg ) - sys.exit() - -def toTar(tarFileName, samOutputNames): - dir = os.path.dirname(tarFileName) - tfile = tarfile.open(tarFileName + ".tmp.tar", "w") - currentPath = os.getcwd() - os.chdir(dir) - for file in samOutputNames: - relativeFileName = os.path.basename(file) - tfile.add(relativeFileName) - os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName)) - tfile.close() - os.chdir(currentPath) - -def _map(iLauncher, cmd, cmdStart, cmdFinish ): - lCmds = [] - lCmds.extend(cmd) - lCmdStart = [] - lCmdStart.extend(cmdStart) - lCmdFinish = [] - lCmdFinish.extend(cmdFinish) - return(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish)) - -def _createSamToolsViewCmd(iLauncher, inputFile, tmp_sorted_aligns_file_name, header): - lArgs = [] - lArgs.append("-o %s" % inputFile) - lArgs.append("%s" % tmp_sorted_aligns_file_name) - if header: - lArgs.append("-h") - return iLauncher.getSystemCommand("samtools view", lArgs) - -def _createSamToolsSortCmd(iLauncher, inputFile, tmp_sorted_aligns_file_base): - lArgs = [] - lArgs.append("%s" % inputFile) - lArgs.append("%s" % tmp_sorted_aligns_file_base) - return iLauncher.getSystemCommand("samtools sort", lArgs) - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option('-t', '--tar', dest='outputTar', default=None, help='output all SAM results in a tar file.' ) - parser.add_option( '', '--input1', dest='input1', help='The input list of BAM datasets on txt format.' ) - #parser.add_option( '', '--input1', dest='input1', help='The input BAM dataset' ) - parser.add_option( '', '--output1', dest='output1', help='The output list of SAM datasets on txt format.' ) - #parser.add_option( '', '--output1', dest='output1', help='The output SAM dataset' ) - parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) - ( options, args ) = parser.parse_args() - - - #Parse the input txt file and read a list of BAM files. - file = open(options.input1, "r") - lines = file.readlines() - inputFileNames = [] - samOutputNames = [] - outputName = options.output1 - resDirName = os.path.dirname(outputName) + '/' - #Write output txt file and define all output sam file names. - out = open(outputName, "w") - for line in lines: - tab = line.split() - inputFileNames.append(tab[1]) - samOutName = resDirName + tab[0] + '_samOutput_%s.sam' % random.randrange(0, 10000) - samOutputNames.append(samOutName) - out.write(tab[0] + '\t' + samOutName + '\n') - file.close() - out.close() - - # output version # of tool - try: - tmp_files = [] - tmp = tempfile.NamedTemporaryFile().name - tmp_files.append(tmp) - tmp_stdout = open( tmp, 'wb' ) - proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout ) - tmp_stdout.close() - returncode = proc.wait() - stdout = None - for line in open( tmp_stdout.name, 'rb' ): - if line.lower().find( 'version' ) >= 0: - stdout = line.strip() - break - if stdout: - sys.stdout.write( 'Samtools %s\n' % stdout ) - else: - raise Exception - except: - sys.stdout.write( 'Could not determine Samtools version\n' ) - - tmp_dirs = [] - acronym = "bam_to_sam" - jobdb = TableJobAdaptatorFactory.createJobInstance() - iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True) - lCmdsTuples = [] - for i in range(len(inputFileNames)): #Construct the lines commands - if os.path.getsize( inputFileNames[i] ) == 0: - raise Exception, 'Initial input txt file is empty.' - tmp_dir = tempfile.mkdtemp(dir="%s" % os.getcwd()) - tmp_dirs.append(tmp_dir) - tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir ) - tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name - tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name - tmp_files.append(tmp_sorted_aligns_file_name) - tmp_sorted_aligns_file.close() - - inputFile = inputFileNames[i] - outputFile = samOutputNames[i] - cmd2Launch = [] - cmd2Launch.append(_createSamToolsSortCmd(iLauncher, inputFile, tmp_sorted_aligns_file_base)) - cmd2Launch.append(_createSamToolsViewCmd(iLauncher, outputFile, tmp_sorted_aligns_file_name, options.header)) - cmdStart = [] - cmdFinish = [] - lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish)) - - iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True) - - if options.outputTar != None: - toTar(options.outputTar, samOutputNames) - #clean up temp files - for tmp_dir in tmp_dirs: - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - #print tmp_files - #for tmp in tmp_files: - # os.remove(tmp) - - -if __name__=="__main__": __main__() |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/bam_to_sam_parallel_unSQL.xml --- a/SMART/DiffExpAnal/bam_to_sam_parallel_unSQL.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,32 +0,0 @@ -<tool id="bam_to_sam_parallel_unSQL" name="BAM to SAM (for DEA in parallel)" version="1.0.0"> - <description>converts a list of BAM format files to SAM format (parallelized).</description> - <requirements> - <requirement type="package">samtools</requirement> - </requirements> - <command interpreter="python"> bam_to_sam_parallel_unSQL.py - --input1=$input1 - --output1=$output1 - $header - $tar $outputTarFile - </command> - <inputs> - <param name="input1" type="data" format="txt" label="BAM File LIST to Convert" /> - <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /> - <param name="tar" type="boolean" truevalue="-t" falsevalue="" checked="false" label="tar option" help="This option creates a tar file for all out results." /> - </inputs> - <outputs> - <data format="txt" name="output1" label="converted SAM LIST files " /> - <data name="outputTarFile" format="tar"> - <filter>tar</filter> - </data> - </outputs> - <help> - -**What it does** - -This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. - -.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml - - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/compareOverlapping_parallel.py --- a/SMART/DiffExpAnal/compareOverlapping_parallel.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,175 +0,0 @@\n-#! /usr/bin/env python\n-#This program is a wrapp for CompareOverlapping.py.\n-import optparse, os, sys, subprocess, tempfile, shutil, tarfile, glob\n-import os, struct, time, random\n-from optparse import OptionParser\n-from commons.core.parsing.ParserChooser import ParserChooser\n-from commons.core.writer.Gff3Writer import Gff3Writer\n-from SMART.Java.Python.CompareOverlapping import CompareOverlapping\n-from SMART.Java.Python.structure.Transcript import Transcript\n-from SMART.Java.Python.structure.Interval import Interval\n-from SMART.Java.Python.ncList.NCList import NCList\n-from SMART.Java.Python.ncList.NCListCursor import NCListCursor\n-from SMART.Java.Python.ncList.NCListFilePickle import NCListFilePickle, NCListFileUnpickle\n-from SMART.Java.Python.ncList.FileSorter import FileSorter\n-from SMART.Java.Python.misc.Progress import Progress\n-from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress\n-from SMART.Java.Python.misc import Utils\n-\n-\n-\n-def stop_err( msg ):\n-\tsys.stderr.write( "%s\\n" % msg )\n-\tsys.exit()\n-\n-def toTar(tarFileName, overlapOutputNames):\n-\tdir = os.path.dirname(tarFileName)\t\n-\ttfile = tarfile.open(tarFileName + ".tmp.tar", "w")\n-\tcurrentPath = os.getcwd()\n-\tos.chdir(dir)\n-\tfor file in overlapOutputNames:\n-\t\trelativeFileName = os.path.basename(file)\n-\t\ttfile.add(relativeFileName)\n-\tos.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))\n-\ttfile.close()\n-\tos.chdir(currentPath)\n-\n-def __main__():\n-\tdescription = "Compare Overlapping wrapp script: Get the a list of data which overlap with a reference set. [Category: Data Comparison]"\n-\tparser = OptionParser(description = description)\n-\tparser.add_option("-i", "--input1",\t\t dest="inputFileName1", action="store",\t\t\t\t\t type="string", help="input file 1 (for annotation) [compulsory] [format: file in transcript format given by -f]")\n-\tparser.add_option("-f", "--format1",\t\t dest="format1",\t\taction="store",\t\t\t\t\t type="string", help="format of file 1 [compulsory] [format: transcript file format]")\n-\tparser.add_option("", "--inputTxt", \t\tdest="inputTxt", \t\taction="store", \t\t\t\ttype="string", \thelp="input, a txt file for a list of input reads files. Should identify all reads files format, given by -g [compulsory]")\n-\t#parser.add_option("-j", "--input2",\t\t dest="inputFileName2", action="store",\tdefault="inputRead",\t type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")\n-\tparser.add_option("-g", "--format2",\t\t dest="format2",\t\taction="store",\t\t\t\t type="string", help="format of file 2 [compulsory] [format: transcript file format]")\n-\t#parser.add_option("-o", "--output",\t\t dest="output",\t\t action="store",\t default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")\n-\tparser.add_option("-S", "--start1",\t\t dest="start1",\t\t action="store",\t default=None, type="int",\thelp="only consider the n first nucleotides of the transcripts in file 1 (do not use it with -U) [format: int]")\n-\tparser.add_option("-s", "--start2",\t\t dest="start2",\t\t action="store",\t default=None, type="int",\thelp="only consider the n first nucleotides of the transcripts in file 2 (do not use it with -u) [format: int]")\n-\tparser.add_option("-U", "--end1",\t\t\t dest="end1",\t\t action="store",\t default=None, type="int",\thelp="only consider the n last nucleotides of the transcripts in file 1 (do not use it with -S) [format: int]")\n-\tparser.add_option("-u", "--end2",\t\t\t dest="end2",\t\t action="store",\t default=None, type="int",\thelp="only consider the n last nucleotides of the transcripts in file 2 (do not use it with -s) [format: int]")\n-\tparser.add_option("-t", "--intron",\t\t dest="introns",\t\taction="store_true", default=False,\t\t\t\thelp="also report introns [format: bool] [default: false]")\n-\tparser.add_option("-E", "--5primeExtension1", dest="fivePrime1",\t action="store",\t default=None, type="int",\thelp="extension towards 5\' in file 1 [format: int]")\n-\tparser.add_option("-e"'..b'verlapping data [format: bool] [default: false]")\n-\tparser.add_option("-x", "--exclude",\t\t dest="exclude",\t\taction="store_true", default=False,\t\t\t\thelp="invert the match [format: bool] [default: false]")\n-\tparser.add_option("-v", "--verbosity",\t\tdest="verbosity",\t action="store",\t default=1,\t type="int",\thelp="trace level [format: int]")\n-\tparser.add_option(\'\', \'--tar\', dest=\'outputTar\', default=None, help=\'output all SAM results in a tar file.\' )\n-\tparser.add_option( \'\', \'--outTxt\', dest=\'outTxtFile\', help=\'The output list of results files on txt format.[compulsory]\' )\n-\t(options, args) = parser.parse_args()\n-\t\n-\t\n-\t#Parse the input txt file and read a list of BAM files.\n-\tfile = open(options.inputTxt, "r")\n-\tlines = file.readlines()\n-\tinputFileNames = []\n-\toverlapOutputNames = []\n-\toutputName = options.outTxtFile\n-\tresDirName = os.path.dirname(outputName) + "/"\n-\t#Write output txt file and define all output sam file names.\n-\tout = open(outputName, "w")\n-\tfor line in lines:\n-\t\ttab = line.split()\n-\t\tinputFileNames.append(tab[1])\n-\t\toverlapOutName = resDirName + tab[0] + \'_overlapOut_%s.gff3\' % random.randrange(0, 10000)\n-\t\toverlapOutputNames.append(overlapOutName)\n-\t\tout.write(tab[0] + \'\\t\' + overlapOutName + \'\\n\')\n-\tfile.close()\n-\tout.close()\n-\t\n-\t#construction the commandes for each input file\n-\tcmds = []\n-\tfor i in range(len(inputFileNames)):\n-\t\tabsFile = sys.argv[0]\n-\t\tabsDir = os.path.dirname(absFile)\n-\t\tparentDir = os.path.abspath(os.path.join(absDir, os.path.pardir))\n-\t\tcmd = "python %s/Java/Python/CompareOverlappingSmallQuery.py " % parentDir\n-\t\topts = "-i %s -f %s -j %s -g %s -o %s " % (options.inputFileName1, options.format1, inputFileNames[i], options.format2, overlapOutputNames[i])\n-\t\t#if options.start1 != None:\n-\t\t#\topts += "-S %s " % options.start1\n-\t\t#if options.start2 != None:\n-\t\t#\topts += "-s %s " % options.start2\n-\t\t#if options.end1 != None:\n-\t\t#\topts += "-U %s " % options.end1\n-\t\t#if options.end2 != None:\n-\t\t#\topts += "-u %s " % options.end2\n-\t\t#if options.fivePrime1 != None:\n-\t\t#\topts += "-E %s " % options.fivePrime1\n-\t\t#if options.fivePrime2 != None:\n-\t\t#\topts += "-e %s " % options.fivePrime2\n-\t\t#if options.threePrime1 != None:\n-\t\t#\topts += "-N %s " % options.threePrime1\n-\t\t#if options.threePrime2 != None:\n-\t\t#\topts += "-n %s " % options.threePrime2\n-\t\t#if options.colinear:\n-\t\t#\topts += "-c "\n-\t\t#if options.antisense:\n-\t\t#\topts +="-a "\n-\t\t#if options.included:\n-\t\t#\topts += "-k "\n-\t\t#if options.including:\n-\t\t#\topts += "-K "\n-\t\t#if options.pcOverlap != None:\n-\t\t#\topts += "-p %s " % options.pcOverlap\n-\t\tif options.notOverlapping:\n-\t\t\topts += "-O "\n-\t\tif options.exclude:\n-\t\t\topts += "-x "\n-\t\tif options.distance != None:\n-\t\t\topts += "-d %s " % options.distance\n-\t\t#if options.minOverlap != None:\n-\t\t#\topts += "-m %s " % options.minOverlap\n-\t\tcmd += opts\n-\t\tcmds.append(cmd)\n-\n-\n-\tprint "les commandes sont %s \\n" % cmds\n-\n-\ttmp_files = []\t\n-\tfor i in range(len(cmds)):\n-\t\ttry:\n-\t\t\ttmp_out = tempfile.NamedTemporaryFile().name\n-\t\t\ttmp_files.append(tmp_out)\n-\t\t\ttmp_stdout = open( tmp_out, \'wb\' )\n-\t\t\ttmp_err = tempfile.NamedTemporaryFile().name\n-\t\t\ttmp_files.append(tmp_err)\n-\t\t\ttmp_stderr = open( tmp_err, \'wb\' )\n-\t\t\tproc = subprocess.Popen( args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )\n-\t\t\treturncode = proc.wait()\n-\t\t\ttmp_stderr.close()\n-\t\t\t# get stderr, allowing for case where it\'s very large\n-\t\t\ttmp_stderr = open( tmp_err, \'rb\' )\n-\t\t\tstderr = \'\'\n-\t\t\tbuffsize = 1048576\n-\t\t\ttry:\n-\t\t\t\twhile True:\n-\t\t\t\t\tstderr += tmp_stderr.read( buffsize )\n-\t\t\t\t\tif not stderr or len( stderr ) % buffsize != 0:\n-\t\t\t\t\t\tbreak\n-\t\t\texcept OverflowError:\n-\t\t\t\tpass\n-\t\t\ttmp_stdout.close()\n-\t\t\ttmp_stderr.close()\n-\t\t\tif returncode != 0:\n-\t\t\t\traise Exception, stderr\n-\t\texcept Exception, e:\n-\t\t\tstop_err( \'Error in :\\n\' + str( e ) )\n-\n-\tif options.outputTar != None:\n-\t\ttoTar(options.outputTar, overlapOutputNames)\t\n-\t\n-\tfor tmp_file in tmp_files:\n-\t\tos.remove(tmp_file)\n-\n-\n-if __name__=="__main__": __main__()\t\t\n-\t\t\n-\t\t\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/compareOverlapping_parallel.xml --- a/SMART/DiffExpAnal/compareOverlapping_parallel.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,251 +0,0 @@\n-<tool id="CompareOverlapping_parallel" name="CompareOverlapping (for DEA)">\n-\t<description>Shrink or extend the sets of genomic coordinates to get the information between starts of reads and starts of genes.</description>\n-\t<command interpreter="python">\n-\t\tcompareOverlapping_parallel.py -i $formatType.inputFileName1\n-\t\t#if $formatType.FormatInputFileName1 == \'bed\':\n-\t\t\t-f bed\n-\t\t#elif $formatType.FormatInputFileName1 == \'gff\':\n-\t\t\t-f gff\t\n-\t\t#elif $formatType.FormatInputFileName1 == \'gff2\':\n-\t\t\t-f gff2\n-\t\t#elif $formatType.FormatInputFileName1 == \'gff3\':\n-\t\t\t-f gff3\n-\t\t#elif $formatType.FormatInputFileName1 == \'sam\':\n-\t\t\t-f sam\n-\t\t#elif $formatType.FormatInputFileName1 == \'gtf\':\n-\t\t\t-f gtf\n-\t\t#end if\n-\t\t\t\n-\t\t--inputTxt $inputTxt \n-\t\t\n-\t\t-g $format2\n-\n-\t\t--outTxt $outTxtFile\n-\n-\t\t#if $optionNFirstFile1.NFirstForFile1 == \'Yes\':\n-\t\t\t-S $optionNFirstFile1.firstNtFile1\n-\t\t#end if\n-\t\t#if $optionNFirstFile2.NFirstForFile2 == \'Yes\':\n-\t\t\t-s $optionNFirstFile2.firstNtFile2\n-\t\t#end if\n-\t\t#if $optionNLastFile1.NLastForFile1 == \'Yes\':\n-\t\t\t-U $optionNLastFile1.lastNtFile1\n-\t\t#end if\n-\t\t#if $optionNLastFile2.NLastForFile2 == \'Yes\':\n-\t\t\t-u $optionNLastFile2.lastNtFile2\n-\t\t#end if\n-\t\n-\t\t#if $optionExtentionCinqFile1.extentionFile1 == \'Yes\':\n-\t\t\t-E $optionExtentionCinqFile1.extention51\n-\t\t#end if\n-\t\t#if $optionExtentionCinqFile2.extentionFile2 == \'Yes\':\n-\t\t\t-e $optionExtentionCinqFile2.extention52\n-\t\t#end if\n-\n-\t\t#if $optionExtentionTroisFile1.extentionFile1 == \'Yes\':\n-\t\t\t-N $optionExtentionTroisFile1.extention31\n-\t\t#end if\n-\t\t#if $optionExtentionTroisFile2.extentionFile2 == \'Yes\':\n-\t\t\t-n $optionExtentionTroisFile2.extention32\n-\t\t#end if\t\n-\n-\t\t#if $OptionColinearOrAntiSens.OptionCA == \'Colinear\':\n-\t\t\t-c \n-\t\t#elif $OptionColinearOrAntiSens.OptionCA == \'AntiSens\':\n-\t\t\t-a\n-\t\t#end if\t\n-\n-\t\t#if $OptionDistance.Dist == \'Yes\':\n-\t\t\t-d $OptionDistance.distance\n-\t\t#end if\n-\n-\t\t#if $OptionMinOverlap.MO == \'Yes\':\n-\t\t\t-m $OptionMinOverlap.minOverlap\n-\t\t#end if\n-\n-\t\t$InvertMatch\n-\t\t$ReportIntron\n-\t\t$NotOverlapping\n-\t\t$tar $outputTarFile\n-\t</command>\n-\n-\t<inputs>\n-\n-\t\t<conditional name="formatType">\n-\t\t\t<param name="FormatInputFileName1" type="select" label="Input File Format 1">\n-\t\t\t\t<option value="bed">bed</option>\n-\t\t\t\t<option value="gff">gff</option>\n-\t\t\t\t<option value="gff2">gff2</option>\n-\t\t\t\t<option value="gff3">gff3</option>\n-\t\t\t\t<option value="sam">sam</option>\n-\t\t\t\t<option value="gtf">gtf</option>\n-\t\t\t</param>\n-\t\t\t<when value="bed">\n-\t\t\t\t<param name="inputFileName1" format="bed" type="data" label="Input File 1"/>\n-\t\t\t</when>\n-\t\t\t<when value="gff">\n-\t\t\t\t<param name="inputFileName1" format="gff" type="data" label="Input File 1"/>\n-\t\t\t</when>\n-\t\t\t<when value="gff2">\n-\t\t\t\t<param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>\n-\t\t\t</when>\n-\t\t\t<when value="gff3">\n-\t\t\t\t<param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>\n-\t\t\t</when>\n-\t\t\t<when value="sam">\n-\t\t\t\t<param name="inputFileName1" format="sam" type="data" label="Input File 1"/>\n-\t\t\t</when>\n-\t\t\t<when value="gtf">\n-\t\t\t\t<param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>\n- </when>\n-\t\t</conditional>\n-\t\t\n-\t\t<param name="inputTxt" type="data" format="txt" label="A txt file contains a list of several input transcripts files." />\n-\t\t\n-\t\t<param name="format2" type="text" value="bed" label="format for File 2, you can choose [bed, gff, gff2, gff3, sam, gtf]"/>\n-\t\t\n-\t\t<conditional name="optionNFirstFile1">\n-\t\t\t<param name="NFirstForFile1" type="select" label="NFirst for file 1" help="only consider the n first nucleotides of the transcripts in file 1">\n-\t\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="firstNtFile1" type="integer" value="1" label="n first nucleotides for input file 1" />\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\t\t<conditional name="optionNFirstFile2">\n-\t\t\t<param name="NFirs'..b'tForFile2" type="select" label="NLast for file 2">\n-\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="lastNtFile2" type="integer" value="1" label="n last nucleotides for input file 2" help="only consider the n last nucleotides of the transcripts in file 2"/>\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="optionExtentionCinqFile1">\n-\t\t\t<param name="extentionFile1" type="select" label="Extension towards 5 for file 1">\n-\t\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="extention51" type="integer" value="1" label="in file 1" />\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="optionExtentionCinqFile2">\n-\t\t\t<param name="extentionFile2" type="select" label="Extension towards 5 for file 2">\n-\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="extention52" type="integer" value="1" label="in file 2"/>\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="optionExtentionTroisFile1">\n-\t\t\t<param name="extentionFile1" type="select" label="Extension towards 3 for file 1">\n-\t\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="extention31" type="integer" value="1" label="in file 1" />\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="optionExtentionTroisFile2">\n-\t\t\t<param name="extentionFile2" type="select" label="Extension towards 3 for file 2">\n-\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="extention32" type="integer" value="1" label="in file 2" />\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="OptionColinearOrAntiSens">\n-\t\t\t<param name="OptionCA" type="select" label="Colinear or anti-sens">\n-\t\t\t\t<option value="Colinear">Colinear</option>\n-\t\t\t\t<option value="AntiSens">AntiSens</option>\n-\t\t\t\t<option value="NONE" selected="true">NONE</option>\n-\t\t\t</param>\n-\t\t\t<when value="Colinear">\n-\t\t\t</when>\n-\t\t\t<when value="AntiSens">\n-\t\t\t</when>\n-\t\t\t<when value="NONE">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="OptionDistance">\n-\t\t\t<param name="Dist" type="select" label="Maximum Distance between two reads">\n-\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="distance" type="integer" value="0"/>\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="OptionMinOverlap">\n-\t\t\t<param name="MO" type="select" label="Minimum number of overlapping between two reads">\n-\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="minOverlap" type="integer" value="1"/>\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\t\t<param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>\n-\t\t<param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Report intron"/>\n-\t\t<param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>\n-\t\t<param name="tar" type="boolean" truevalue="--tar" falsevalue="" checked="false" label="tar option" help="This option creates a tar file for all out results." />\n-\t</inputs>\n-\n-\t<outputs>\n-\t\t<data name="outTxtFile" format="txt" label="overlapping output files "/>\n-\t\t<data name="outputTarFile" format="tar">\n-\t\t <filter>tar</filter>\n-\t </data>\n-\t</outputs> \n-\t\n-</tool>\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/compareOverlapping_parallel_unSQL.py --- a/SMART/DiffExpAnal/compareOverlapping_parallel_unSQL.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,205 +0,0 @@\n-#! /usr/bin/env python\n-#This program is a wrapp for CompareOverlapping.py.\n-import os, sys, tarfile, optparse\n-from commons.core.launcher.Launcher import Launcher\n-from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory\n-from optparse import OptionParser\n-from commons.core.utils.FileUtils import FileUtils\n-from commons.core.parsing.ParserChooser import ParserChooser\n-from SMART.Java.Python.structure.TranscriptList import TranscriptList\n-from commons.core.writer.WriterChooser import WriterChooser\n-\n-def stop_err( msg ):\n-\tsys.stderr.write( "%s\\n" % msg )\n-\tsys.exit()\n-\n-def toTar(tarFileName, overlapOutputNames):\n-\tdir = os.path.dirname(tarFileName)\t\n-\ttfile = tarfile.open(tarFileName + ".tmp.tar", "w")\n-\tcurrentPath = os.getcwd()\n-\tos.chdir(dir)\n-\tfor file in overlapOutputNames:\n-\t\trelativeFileName = os.path.basename(file)\n-\t\ttfile.add(relativeFileName)\n-\tos.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))\n-\ttfile.close()\n-\tos.chdir(currentPath)\n-\n-def _createCompareOverlappingCmd(iLauncher, options, inputFileName, annotationFile, overlapOutputName):\n-\tlArgs = []\n-\tlArgs.append("-i %s" % annotationFile)\n-\tlArgs.append("-f %s" % options.format1)\n-\tlArgs.append("-j %s" % inputFileName)\n-\tlArgs.append("-g %s" % options.format2)\n-\tlArgs.append("-o %s" % overlapOutputName)\n-\tif options.notOverlapping:\n-\t\tlArgs.append("-O")\n-\tif options.exclude:\n-\t\tlArgs.append("-x")\n-\tif options.distance != None:\n-\t\tlArgs.append("-d %s" % options.distance)\n-\treturn(iLauncher.getSystemCommand("python %s/SMART/Java/Python/CompareOverlappingSmallQuery.py" % os.environ["REPET_PATH"], lArgs))\n-\n-def _map(iLauncher, cmd, cmdStart, cmdFinish ):\n-\tlCmds = []\n-\tlCmds.append(cmd)\n-\tlCmdStart = []\n-\tlCmdStart.append(cmdStart)\n-\tlCmdFinish = []\n-\tlCmdFinish.append(cmdFinish)\n-\treturn(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))\n-\n-def split(fileName, nbOfSeqPerBatch):\n-\tfilePrefix, fileExt = os.path.splitext(os.path.basename(fileName))\n-\tresDir = os.path.dirname(fileName)\n-\tlInputName = []\n-\tfileNb = 1\n-\tSeqNb = 0\n-\toutFileName = "%s/%s-%s%s" %(resDir, filePrefix, fileNb, fileExt)\n-\tlInputName.append(outFileName)\n-\toutFile = open(outFileName, "w")\n-\tf = open(fileName, "r")\n-\tline = f.readline()\n-\tpreviousRefName = ""\n-\twhile line != "":\n-\t\tif not line.startswith(\'@SQ\'):\n-\t\t\tif SeqNb == nbOfSeqPerBatch:\n-\t\t\t\tSeqNb = 0\n-\t\t\t\tfileNb += 1\n-\t\t\t\toutFile.close()\n-\t\t\t\toutFileName = "%s/%s-%s%s" %(resDir, filePrefix, fileNb, fileExt)\n-\t\t\t\tlInputName.append(outFileName)\n-\t\t\t\toutFile = open(outFileName, "w")\n-\t\t\trefName = line.split("\\t")[2]\n-\t\t\tif previousRefName != refName:\n-\t\t\t\tSeqNb += 1\n-\t\t\t\toutFile.write(line)\n-\t\t\telse:\n-\t\t\t\tpreviousRefName = refName\n-\t\t\t\toutFile.write(line)\n-\t\tline = f.readline()\n-\treturn lInputName\t\t\n-\n-def join(dCutOut2Out, options):\n-\tchooser = ParserChooser()\n-\tchooser.findFormat("gtf")\n-\tgtfParser = chooser.getParser(options.inputFileName1)\n-\tref = {}\n-\tfor transcript in gtfParser.getIterator():\n-\t\tref[transcript.getTagValue("ID")] = transcript\n-\tfor key in dCutOut2Out.keys():\n-\t\twriterChooser = WriterChooser()\n-\t\twriterChooser.findFormat("gff3")\n-\t\tfor inputFile in dCutOut2Out[key]:\n-\t\t\tchooser = ParserChooser()\n-\t\t\tchooser.findFormat("gff")\n-\t\t\tgffParser = chooser.getParser(inputFile)\n-\t\t\tfor transcript in gffParser.getIterator():\n-\t\t\t\t\tfinalTranscript = ref[transcript.getTagValue("ID")]\n-\t\t\t\t\tif finalTranscript.getTagValue("nbOverlaps"):\n-\t\t\t\t\t\tnbOverlap = int(finalTranscript.getTagValue("nbOverlaps")) + int(transcript.getTagValue("nbOverlaps"))\n-\t\t\t\t\t\tfinalTranscript.setTagValue("nbOverlaps", nbOverlap)\n-\t\t\t\t\telse:\n-\t\t\t\t\t\tfinalTranscript.setTagValue("nbOverlaps", transcript.getTagValue("nbOverlaps"))\n-\t\t\t\t\t\n-\t\t\t\t\tif finalTranscript.getTagValue("overlapsWith") and transcript.getTagValue("overlapsWith") != None:\n-\t\t\t\t\t\toverlapName = "--".join([finalTranscript.getTagValue("overlapsWith"), transcript.getTagValue("overlapsWith")])\n-\t\t\t\t\t\tfinalTranscript.set'..b'pe="int",\thelp="extension towards 3\' in file 2 [format: int]")\n-\tparser.add_option("-c", "--colinear",\t\t dest="colinear",\t action="store_true", default=False,\t\t\t\thelp="colinear only [format: bool] [default: false]")\n-\tparser.add_option("-a", "--antisense",\t\tdest="antisense",\t action="store_true", default=False,\t\t\t\thelp="antisense only [format: bool] [default: false]")\n-\tparser.add_option("-d", "--distance",\t\t dest="distance",\t action="store",\t default=None,\t type="int",\thelp="accept some distance between query and reference [format: int]")\n-\tparser.add_option("-k", "--included",\t\t dest="included",\t action="store_true", default=False,\t\t\t\thelp="keep only elements from file 1 which are included in an element of file 2 [format: bool] [default: false]")\n-\tparser.add_option("-K", "--including",\t\tdest="including",\t action="store_true", default=False,\t\t\t\thelp="keep only elements from file 2 which are included in an element of file 1 [format: bool] [default: false]")\n-\tparser.add_option("-m", "--minOverlap",\t dest="minOverlap",\t action="store",\t default=None,\t type="int",\thelp="minimum number of nucleotides overlapping to declare an overlap [format: int] [default: 1]")\n-\tparser.add_option("-p", "--pcOverlap",\t\tdest="pcOverlap",\t action="store",\t default=None, type="int",\thelp="minimum percentage of nucleotides to overlap to declare an overlap [format: int]")\n-\tparser.add_option("-O", "--notOverlapping", dest="notOverlapping", action="store_true", default=False,\t\t\t\thelp="also output not overlapping data [format: bool] [default: false]")\n-\tparser.add_option("-x", "--exclude",\t\t dest="exclude",\t\taction="store_true", default=False,\t\t\t\thelp="invert the match [format: bool] [default: false]")\n-\tparser.add_option("-v", "--verbosity",\t\tdest="verbosity",\t action="store",\t default=1,\t type="int",\thelp="trace level [format: int]")\n-\tparser.add_option(\'\', \'--tar\', dest=\'outputTar\', default=None, help=\'output all SAM results in a tar file.\' )\n-\tparser.add_option( \'\', \'--outTxt\', dest=\'outTxtFile\', help=\'The output list of results files on txt format.[compulsory]\' )\n-\t(options, args) = parser.parse_args()\n-\t\n-\t\n-\t#Parse the input txt file and read a list of BAM files.\n-\tfile = open(options.inputTxt, "r")\n-\tlines = file.readlines()\n-\tinputFileNames = []\n-\toverlapOutputNames = []\n-\toutputName = options.outTxtFile\n-\tresDirName = os.path.dirname(outputName) + "/"\n-\t#Write output txt file and define all output sam file names.\n-\tout = open(outputName, "w")\n-\tfor line in lines:\n-\t\ttab = line.split()\n-\t\tinputFileNames.append(tab[1])\n-\t\toverlapOutName = resDirName + tab[0] + \'_overlapOut.gff3\'\n-\t\toverlapOutputNames.append(overlapOutName)\n-\t\tout.write(tab[0] + \'\\t\' + overlapOutName + \'\\n\')\n-\tfile.close()\n-\tout.close()\n-\t\n-\t#Launch on nodes\n-\tacronym = "compareOverlapping"\n-\tjobdb = TableJobAdaptatorFactory.createJobInstance()\n-\tiLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "test", acronym, acronym, False, True)\n-\n-\n-\t\n-\n-\t#construction the commandes for each input file\n-\tlCmdsTuples = []\n-\tdCutOut2Out = {}\n-\tlAllFile2remove = []\n-\tfor i in range(len(inputFileNames)):\n-\t\tlCutInputFile = split(inputFileNames[i], 20000)\n-\t\tlAllFile2remove.extend(lCutInputFile)\n-\t\tlCutOutput = []\n-\t\tfor cutInput in lCutInputFile:\n-\t\t\tcutOutput = "%s_out" % cutInput\n-\t\t\tlCutOutput.append(cutOutput)\n-\t\t\tlAllFile2remove.extend(lCutOutput)\n-\t\t\tcmd2Launch = _createCompareOverlappingCmd(iLauncher, options, cutInput, options.inputFileName1, cutOutput)\n-\t\t\tlCmdsTuples.append(_map(iLauncher, cmd2Launch, "", ""))\n-\t\tchooser = ParserChooser()\n-\t\tchooser.findFormat(options.format2)\n-\t\tdCutOut2Out[overlapOutputNames[i]] = lCutOutput\n-\tiLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True)\n-\t\n-\tjoin(dCutOut2Out, options)\n-\tFileUtils.removeFilesFromListIfExist(lAllFile2remove)\n-\n-\tif options.outputTar != None:\n-\t\ttoTar(options.outputTar, overlapOutputNames)\t\n-\n-if __name__=="__main__": __main__()\t\t\n\\ No newline at end of file\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/compareOverlapping_parallel_unSQL.xml --- a/SMART/DiffExpAnal/compareOverlapping_parallel_unSQL.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,251 +0,0 @@\n-<tool id="CompareOverlapping_parallel_unSQL" name="CompareOverlapping (for DEA in parallel)">\n-\t<description>Shrink or extend the sets of genomic coordinates to get the information between starts of reads and starts of genes (parallelized).</description>\n-\t<command interpreter="python">\n-\t\tcompareOverlapping_parallel_unSQL.py -i $formatType.inputFileName1\n-\t\t#if $formatType.FormatInputFileName1 == \'bed\':\n-\t\t\t-f bed\n-\t\t#elif $formatType.FormatInputFileName1 == \'gff\':\n-\t\t\t-f gff\t\n-\t\t#elif $formatType.FormatInputFileName1 == \'gff2\':\n-\t\t\t-f gff2\n-\t\t#elif $formatType.FormatInputFileName1 == \'gff3\':\n-\t\t\t-f gff3\n-\t\t#elif $formatType.FormatInputFileName1 == \'sam\':\n-\t\t\t-f sam\n-\t\t#elif $formatType.FormatInputFileName1 == \'gtf\':\n-\t\t\t-f gtf\n-\t\t#end if\n-\t\t\t\n-\t\t--inputTxt $inputTxt \n-\t\t\n-\t\t-g $format2\n-\n-\t\t--outTxt $outTxtFile\n-\n-\t\t#if $optionNFirstFile1.NFirstForFile1 == \'Yes\':\n-\t\t\t-S $optionNFirstFile1.firstNtFile1\n-\t\t#end if\n-\t\t#if $optionNFirstFile2.NFirstForFile2 == \'Yes\':\n-\t\t\t-s $optionNFirstFile2.firstNtFile2\n-\t\t#end if\n-\t\t#if $optionNLastFile1.NLastForFile1 == \'Yes\':\n-\t\t\t-U $optionNLastFile1.lastNtFile1\n-\t\t#end if\n-\t\t#if $optionNLastFile2.NLastForFile2 == \'Yes\':\n-\t\t\t-u $optionNLastFile2.lastNtFile2\n-\t\t#end if\n-\t\n-\t\t#if $optionExtentionCinqFile1.extentionFile1 == \'Yes\':\n-\t\t\t-E $optionExtentionCinqFile1.extention51\n-\t\t#end if\n-\t\t#if $optionExtentionCinqFile2.extentionFile2 == \'Yes\':\n-\t\t\t-e $optionExtentionCinqFile2.extention52\n-\t\t#end if\n-\n-\t\t#if $optionExtentionTroisFile1.extentionFile1 == \'Yes\':\n-\t\t\t-N $optionExtentionTroisFile1.extention31\n-\t\t#end if\n-\t\t#if $optionExtentionTroisFile2.extentionFile2 == \'Yes\':\n-\t\t\t-n $optionExtentionTroisFile2.extention32\n-\t\t#end if\t\n-\n-\t\t#if $OptionColinearOrAntiSens.OptionCA == \'Colinear\':\n-\t\t\t-c \n-\t\t#elif $OptionColinearOrAntiSens.OptionCA == \'AntiSens\':\n-\t\t\t-a\n-\t\t#end if\t\n-\n-\t\t#if $OptionDistance.Dist == \'Yes\':\n-\t\t\t-d $OptionDistance.distance\n-\t\t#end if\n-\n-\t\t#if $OptionMinOverlap.MO == \'Yes\':\n-\t\t\t-m $OptionMinOverlap.minOverlap\n-\t\t#end if\n-\n-\t\t$InvertMatch\n-\t\t$ReportIntron\n-\t\t$NotOverlapping\n-\t\t$tar $outputTarFile\n-\t</command>\n-\n-\t<inputs>\n-\n-\t\t<conditional name="formatType">\n-\t\t\t<param name="FormatInputFileName1" type="select" label="Input File Format 1">\n-\t\t\t\t<option value="bed">bed</option>\n-\t\t\t\t<option value="gff">gff</option>\n-\t\t\t\t<option value="gff2">gff2</option>\n-\t\t\t\t<option value="gff3">gff3</option>\n-\t\t\t\t<option value="sam">sam</option>\n-\t\t\t\t<option value="gtf">gtf</option>\n-\t\t\t</param>\n-\t\t\t<when value="bed">\n-\t\t\t\t<param name="inputFileName1" format="bed" type="data" label="Input File 1"/>\n-\t\t\t</when>\n-\t\t\t<when value="gff">\n-\t\t\t\t<param name="inputFileName1" format="gff" type="data" label="Input File 1"/>\n-\t\t\t</when>\n-\t\t\t<when value="gff2">\n-\t\t\t\t<param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>\n-\t\t\t</when>\n-\t\t\t<when value="gff3">\n-\t\t\t\t<param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>\n-\t\t\t</when>\n-\t\t\t<when value="sam">\n-\t\t\t\t<param name="inputFileName1" format="sam" type="data" label="Input File 1"/>\n-\t\t\t</when>\n-\t\t\t<when value="gtf">\n-\t\t\t\t<param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>\n- </when>\n-\t\t</conditional>\n-\t\t\n-\t\t<param name="inputTxt" type="data" format="txt" label="A txt file contains a list of several input transcripts files." />\n-\t\t\n-\t\t<param name="format2" type="text" value="bed" label="format for File 2, you can choose [bed, gff, gff2, gff3, sam, gtf]"/>\n-\t\t\n-\t\t<conditional name="optionNFirstFile1">\n-\t\t\t<param name="NFirstForFile1" type="select" label="NFirst for file 1" help="only consider the n first nucleotides of the transcripts in file 1">\n-\t\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="firstNtFile1" type="integer" value="1" label="n first nucleotides for input file 1" />\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\t\t<conditional name="opt'..b'tForFile2" type="select" label="NLast for file 2">\n-\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="lastNtFile2" type="integer" value="1" label="n last nucleotides for input file 2" help="only consider the n last nucleotides of the transcripts in file 2"/>\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="optionExtentionCinqFile1">\n-\t\t\t<param name="extentionFile1" type="select" label="Extension towards 5 for file 1">\n-\t\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="extention51" type="integer" value="1" label="in file 1" />\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="optionExtentionCinqFile2">\n-\t\t\t<param name="extentionFile2" type="select" label="Extension towards 5 for file 2">\n-\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="extention52" type="integer" value="1" label="in file 2"/>\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="optionExtentionTroisFile1">\n-\t\t\t<param name="extentionFile1" type="select" label="Extension towards 3 for file 1">\n-\t\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="extention31" type="integer" value="1" label="in file 1" />\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="optionExtentionTroisFile2">\n-\t\t\t<param name="extentionFile2" type="select" label="Extension towards 3 for file 2">\n-\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="extention32" type="integer" value="1" label="in file 2" />\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="OptionColinearOrAntiSens">\n-\t\t\t<param name="OptionCA" type="select" label="Colinear or anti-sens">\n-\t\t\t\t<option value="Colinear">Colinear</option>\n-\t\t\t\t<option value="AntiSens">AntiSens</option>\n-\t\t\t\t<option value="NONE" selected="true">NONE</option>\n-\t\t\t</param>\n-\t\t\t<when value="Colinear">\n-\t\t\t</when>\n-\t\t\t<when value="AntiSens">\n-\t\t\t</when>\n-\t\t\t<when value="NONE">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="OptionDistance">\n-\t\t\t<param name="Dist" type="select" label="Maximum Distance between two reads">\n-\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="distance" type="integer" value="0"/>\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\n-\t\t<conditional name="OptionMinOverlap">\n-\t\t\t<param name="MO" type="select" label="Minimum number of overlapping between two reads">\n-\t\t\t\t<option value="Yes">Yes</option>\n-\t\t\t\t<option value="No" selected="true">No</option>\n-\t\t\t</param>\n-\t\t\t<when value="Yes">\n-\t\t\t\t<param name="minOverlap" type="integer" value="1"/>\n-\t\t\t</when>\n-\t\t\t<when value="No">\n-\t\t\t</when>\n-\t\t</conditional>\n-\t\t<param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>\n-\t\t<param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Report intron"/>\n-\t\t<param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>\n-\t\t<param name="tar" type="boolean" truevalue="--tar" falsevalue="" checked="false" label="tar option" help="This option creates a tar file for all out results." />\n-\t</inputs>\n-\n-\t<outputs>\n-\t\t<data name="outTxtFile" format="txt" label="overlapping output files "/>\n-\t\t<data name="outputTarFile" format="tar">\n-\t\t <filter>tar</filter>\n-\t </data>\n-\t</outputs> \n-\t\n-</tool>\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/countNumber.pl --- a/SMART/DiffExpAnal/countNumber.pl Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,34 +0,0 @@ -#!/usr/bin/perl -w - -use strict; - -my $in_file = $ARGV[0]; -my $out_file = $ARGV[1]; -my $sort_type = $ARGV[2]; # n(umeric) or a(lphanumeric) -my ($line,$ID,$nbOverlaps,%hash); - -open(IN, $in_file); -while ($line = <IN>){ - chomp($line); - $line=~s/\t/|/g; - my @part=split(/\|/,$line); - my @split=split(";",$part[$#part]); - $split[0] =~ m/^(\w+).+$/; - - foreach my $i (@split){ - if ($i=~m/nbOverlaps=(.+)/){ - $nbOverlaps=$1; - } - if ($i=~m/gene_id=(.+)/){ - $ID=$1; - $hash{$ID}=$nbOverlaps; - } - } -} -close(IN); - -open(OUT, ">$out_file"); -foreach my $key ( sort keys %hash) { - print OUT "$key\t$hash{$key}\n"; -} -close(OUT); |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/countNumber.xml --- a/SMART/DiffExpAnal/countNumber.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,16 +0,0 @@ -<tool id="countNumber" name="countNumber"> - <description>Calculate the number of reads(annotations) overlapping for each transcript.</description> - <command interpreter="perl"> countNumber.pl $input $outputCSV - </command> - - <inputs> - <param name="input" type="data" format="gff3" label="Please choose your gff3 format file (which contains the number of overlaps)."/> - </inputs> - - <outputs> - <data format="csv" name="outputCSV" label="countNumber Output"/> - </outputs> - - <help> - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/countNumber_parallel.py --- a/SMART/DiffExpAnal/countNumber_parallel.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,96 +0,0 @@ -#! /usr/bin/env python - - -import optparse, os, sys, subprocess, tempfile, shutil, tarfile, random -from optparse import OptionParser - -def stop_err(msg): - sys.stderr.write('%s\n' % msg) - sys.exit() - -def toTar(tarFileName, outCountNames): - dir = os.path.dirname(tarFileName) - tfile = tarfile.open(tarFileName + ".tmp.tar", "w") - currentPath = os.getcwd() - os.chdir(dir) - for file in outCountNames: - relativeFileName = os.path.basename(file) - tfile.add(relativeFileName) - os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName)) - tfile.close() - os.chdir(currentPath) - - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option("-i", "--input", dest="inputFile", help="input txt file, a list of overlapping results files.") - parser.add_option("-o", "--output", dest="outputFile", help="Out txt file.") - parser.add_option("-t", "--tar", dest="outputTar", default=None, help="output all count results in a tar file.") - (options, args) = parser.parse_args() - - #Parse the input txt file and read a list of transcripts files. - file = open(options.inputFile, "r") - lines = file.readlines() - inputFileNames = [] - outCountNames = [] - outputName = options.outputFile - resDirName = os.path.dirname(outputName) + '/' - - #Write output txt file and define all output count file names - out = open(outputName, "w") - out.write("label\tfiles\tgroup\n") - for line in lines: - tab = line.split() - inputFileNames.append(tab[1]) - outCountName = resDirName + tab[0] + "_outCount_%s.csv" % random.randrange(0, 10000) - outCountNames.append(outCountName) - out.write(tab[0] + '\t' + outCountName + '\t' + tab[0][5] + '\n') - file.close() - out.close() - - #Construct the lines commands - cmds = [] - for i in range(len(inputFileNames)): - cmd = "perl %s/SMART/DiffExpAnal/countNumber.pl " % os.environ["REPET_PATH"] - opts = "%s %s " % (inputFileNames[i], outCountNames[i]) - cmd += opts - cmds.append(cmd) - - tmp_files = [] - for i in range(len(cmds)): - try: - tmp_out = tempfile.NamedTemporaryFile().name - tmp_files.append(tmp_out) - tmp_stdout = open(tmp_out, 'wb') - tmp_err = tempfile.NamedTemporaryFile().name - tmp_files.append(tmp_err) - tmp_stderr = open(tmp_err, 'wb') - proc = subprocess.Popen(args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr) - returncode = proc.wait() - tmp_stderr.close() - #get stderr, allowing for case where it's very large - tmp_stderr = open(tmp_err, 'rb') - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read(buffsize) - if not stderr or len(stderr) % buffsize != 0: - break - except OverflowError: - pass - tmp_stdout.close() - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - except Exception, e: - stop_err('Error in :\n' + str(e)) - - if options.outputTar != None: - toTar(options.outputTar, outCountNames) - - for tmp_file in tmp_files: - os.remove(tmp_file) - -if __name__=="__main__":__main__() |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/countNumber_parallel.xml --- a/SMART/DiffExpAnal/countNumber_parallel.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,19 +0,0 @@ -<tool id="countNumber_parallel" name="countNumber (for DEA)"> - - <description>Calculate the number of reads(annotations) overlapping for each transcript.</description> - <command interpreter="python"> countNumber_parallel.py -i $inputTxt -o $outputTxt $tar $outputTarFile - </command> - - <inputs> - <param name="inputTxt" type="data" format="txt" label="Please choose your txt format file (which contains a list of gff3 overlapping results files)."/> - <param name="tar" type="boolean" truevalue="-t" falsevalue="" checked="False" label="tar option" help="This option creates a tar file for all out results" /> - </inputs> - - <outputs> - <data format="txt" name="outputTxt" label="countNumber Output"/> - <data name="outputTarFile" format="tar"> - <filter>tar</filter> - </data> - </outputs> - -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/countNumber_parallel_unSQL.py --- a/SMART/DiffExpAnal/countNumber_parallel_unSQL.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,91 +0,0 @@ -#! /usr/bin/env python - - -import optparse, os, sys, tarfile, random -from optparse import OptionParser -from commons.core.launcher.Launcher import Launcher -from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory - -def stop_err(msg): - sys.stderr.write('%s\n' % msg) - sys.exit() - -def toTar(tarFileName, outCountNames): - dir = os.path.dirname(tarFileName) - tfile = tarfile.open(tarFileName + ".tmp.tar", "w") - currentPath = os.getcwd() - os.chdir(dir) - for file in outCountNames: - relativeFileName = os.path.basename(file) - tfile.add(relativeFileName) - os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName)) - tfile.close() - os.chdir(currentPath) - -def _map(iLauncher, cmd, cmdStart, cmdFinish ): - lCmds = [] - lCmds.append(cmd) - lCmdStart = [] - lCmdStart.append(cmdStart) - lCmdFinish = [] - lCmdFinish.append(cmdFinish) - return(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish)) - -def _createCountNumberCommand(iLauncher, inputFile, outputFile): - lArgs = [] - lArgs.append("%s" % inputFile) - lArgs.append("%s" % outputFile) - return iLauncher.getSystemCommand("perl %s/SMART/DiffExpAnal/countNumber.pl " % os.environ["REPET_PATH"], lArgs) - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option("-i", "--input", dest="inputFile", help="input txt file, a list of overlapping results files.") - parser.add_option("-o", "--output", dest="outputFile", help="Out txt file.") - parser.add_option("-t", "--tar", dest="outputTar", default=None, help="output all count results in a tar file.") - (options, args) = parser.parse_args() - - #Parse the input txt file and read a list of transcripts files. - file = open(options.inputFile, "r") - lines = file.readlines() - inputFileNames = [] - outCountNames = [] - outputName = options.outputFile - resDirName = os.path.dirname(outputName) + '/' - - #Write output txt file and define all output count file names - out = open(outputName, "w") - out.write("label\tfiles\tgroup\n") - for line in lines: - tab = line.split() - inputFileNames.append(tab[1]) - outCountName = resDirName + tab[0] + "_outCount_%s.csv" % random.randrange(0, 10000) - outCountNames.append(outCountName) - out.write(tab[0] + '\t' + outCountName + '\t' + tab[0][5] + '\n') - file.close() - out.close() - - #Launch on nodes - acronym = "countNumber" - jobdb = TableJobAdaptatorFactory.createJobInstance() - iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True) - lCmdsTuples = [] - for i in range(len(inputFileNames)): #Construct the lines commands - inputFile = inputFileNames[i] - outputFile = outCountNames[i] - cmd2Launch = _createCountNumberCommand(iLauncher, inputFile, outputFile) - cmdStart = "" - cmdFinish = "" - lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish)) - - - - iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True) - - - - if options.outputTar != None: - toTar(options.outputTar, outCountNames) - - -if __name__=="__main__":__main__() |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/countNumber_parallel_unSQL.xml --- a/SMART/DiffExpAnal/countNumber_parallel_unSQL.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,19 +0,0 @@ -<tool id="countNumber_parallel_unSQL" name="countNumber (for DEA in parallel)"> - - <description>Calculate the number of reads(annotations) overlapping for each transcript (parallelized).</description> - <command interpreter="python"> countNumber_parallel_unSQL.py -i $inputTxt -o $outputTxt $tar $outputTarFile - </command> - - <inputs> - <param name="inputTxt" type="data" format="txt" label="Please choose your txt format file (which contains a list of gff3 overlapping results files)."/> - <param name="tar" type="boolean" truevalue="-t" falsevalue="" checked="False" label="tar option" help="This option creates a tar file for all out results" /> - </inputs> - - <outputs> - <data format="txt" name="outputTxt" label="countNumber Output"/> - <data name="outputTarFile" format="tar"> - <filter>tar</filter> - </data> - </outputs> - -</tool> |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/deseq.sh --- a/SMART/DiffExpAnal/deseq.sh Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,21 +0,0 @@ -#! /bin/sh - -#Arguments : -#$1=targetFile(the list of files) -#$2=with or without header -#$3=with or without replicates -#$4=OUT_HTML.html -#$5=OUT_HTML images directory -#$6=OUT_complete.xls -#$7=OUT_up.xls -#$8=OUT_down.xls - -#run example: -#bash deseq.sh DESeqTools/targetTest.txt 1 1 testOUT_HTML.html /tmp/ testOUT_complet.xls testOUT_up.xls testOUT_down.xls - -#echo $5 -#mkdir -p $5 #First, create the images tmp directory given by Galaxy, -p option can create the parent directory which dosen't exist. - -mkdir -p $5 -MY_PATH=`dirname $0` -cat $MY_PATH/DESeqTools/anadiffGenes2conds.R | R --slave --args $1 $2 $3 $4 $5 $6 $7 $8 $0 < $MY_PATH/DESeqTools/anadiffGenes2conds.R |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/deseq.xml --- a/SMART/DiffExpAnal/deseq.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,22 +0,0 @@ -<tool id="DESEQ" name="DESEQ for differential expression analysis"> - <description>Differential expression analysis for reads count data</description> - <command interpreter="bash"> deseq.sh $inputFile $header $withOutReplicates $outHTML $outHTML.files_path $outComplete $outUP $outDown 2> $log </command> - - <inputs> - <param name="inputFile" type="data" label="Input File list" format="txt"/> - <param name="header" type="boolean" truevalue="1" falsevalue="0" checked="false" label="If there is a header for your count files, please choose this case."/> - <param name="withOutReplicates" type="boolean" truevalue="1" falsevalue="0" checked="false" label="If your data has not replicates, please choose this case."/> - - </inputs> - - <outputs> - <data format="HTML" name="outHTML" label="[DESEQ] Output HTML File" help="This output file shows all results images by DESeq analysis"/> - <data format="tabular" name="outComplete" label="[DESEQ] Output complete File"/> - <data format="tabular" name="outUP" label="[DESEQ] Output up File" help="This output file shows the genes of group1 which are overexpressed than those of group2"/> - <data format="tabular" name="outDown" label="[DESEQ] Output down File" help="This output file shows the genes of group1 which are less expressed than those of group2"/> - <data format="txt" name="log" label="[DESEQ] Output log File"/> - </outputs> - - <help> - </help> -</tool> |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/fastq_groomer_parallel.py --- a/SMART/DiffExpAnal/fastq_groomer_parallel.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,115 +0,0 @@ -import sys, os, optparse, random -from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter - -def stop_err(msg): - sys.stderr.write("%s\n" % msg) - sys.exit() - -def main(): - - input_filename = sys.argv[1] #a txt file - input_type = sys.argv[2] - output_filename = sys.argv[3] #a txt file - output_type = sys.argv[4] - force_quality_encoding = sys.argv[5] - summarize_input = sys.argv[6] == 'summarize_input' - pairedEnd_input = sys.argv[7] - if pairedEnd_input == 'None': - pairedEnd_input = None - else: - output_pairedEndFileName = sys.argv[8] - - if force_quality_encoding == 'None': - force_quality_encoding = None - - #Parse the input txt file and read a list of fastq files - file = open(input_filename, "r") - lines = file.readlines() - inputFileNames = [] - outGroomerNames = [] - resDirName = os.path.dirname(output_filename) + "/" - #Write output txt file and define all output groomer file names - outFile = open(output_filename, "w") - for line in lines: - tab = line.split() - inputFileNames.append(tab[1]) - outGroomerName = resDirName + tab[0] + '_outGroomer_%s.fastq' % random.randrange(0, 10000) - outGroomerNames.append(outGroomerName) - outFile.write(tab[0] + '\t' + outGroomerName + '\n') - outFile.close() - file.close() - - if pairedEnd_input != None: - inPairedFile = open(pairedEnd_input, "r") - lines = inPairedFile.readlines() - inputPairedEndFileNames = [] - outGroomerPairedEndNames = [] - outPairedEndFile = open(output_pairedEndFileName, "w") - for line in lines: - tab = line.split() - inputPairedEndFileNames.append(tab[1]) - outGroomerPairedEndName = resDirName + tab[0] + '_outGroomer_pairedEnd_%s.fastq' % random.randrange(0, 10000) - outGroomerPairedEndNames.append(outGroomerPairedEndName) - outPairedEndFile.write(tab[0] + '\t' + outGroomerPairedEndName + '\n') - outPairedEndFile.close() - inPairedFile.close() - - # Write output file - aggregator = fastqAggregator() - for i in range(len(outGroomerNames)): - out = fastqWriter( open( outGroomerNames[i], 'wb' ), format = output_type, force_quality_encoding = force_quality_encoding ) - read_count = None - if summarize_input: - reader = fastqVerboseErrorReader - else: - reader = fastqReader - for read_count, fastq_read in enumerate( reader( open( inputFileNames[i] ), format = input_type, apply_galaxy_conventions = True ) ): - if summarize_input: - aggregator.consume_read( fastq_read ) - out.write( fastq_read ) - out.close() - - if read_count is not None: - print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type ) - if input_type != output_type and 'solexa' in [ input_type, output_type ]: - print "Converted between Solexa and PHRED scores." - if summarize_input: - print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() ) or "None" ) - ascii_range = aggregator.get_ascii_range() - decimal_range = aggregator.get_decimal_range() - print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed - print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] ) - else: - print "No valid FASTQ reads were provided." - - - # Write output pairedEnd file - if pairedEnd_input != None: - aggregator = fastqAggregator() - for i in range(len(outGroomerPairedEndNames)): - outPair = fastqWriter(open(outGroomerPairedEndNames[i], 'wb'), format = output_type, force_quality_encoding = force_quality_encoding) - read_count = None - if summarize_input: - reader = fastqVerboseErrorReader - else: - reader = fastqReader - for read_count, fastq_reader in enumerate(reader(open(inputPairedEndFileNames[i]), format=input_type, apply_galaxy_conventions=True)): - if summarize_input: - aggregator.consume_read(fastq_read) - outPair.write(fastq_read) - outPair.close() - - if read_count is not None: - print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type ) - if input_type != output_type and 'solexa' in [ input_type, output_type ]: - print "Converted between Solexa and PHRED scores." - if summarize_input: - print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() ) or "None" ) - ascii_range = aggregator.get_ascii_range() - decimal_range = aggregator.get_decimal_range() - print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed - print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] ) - else: - print "No valid paired-end FASTQ reads were provided." - -if __name__ == "__main__": main() |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/fastq_groomer_parallel.xml --- a/SMART/DiffExpAnal/fastq_groomer_parallel.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,122 +0,0 @@ -<tool id="fastq_groomer_parallel" name="FASTQ Groomer (for DEA)" version="1.0.0"> - <description>convert between various FASTQ quality formats for a list of inputs.</description> - <command interpreter="python">fastq_groomer_parallel.py '$input_file' '$input_type' '$output_file' -#if str( $options_type['options_type_selector'] ) == 'basic': -#if str( $input_type ) == 'cssanger': -'cssanger' -#else: -'sanger' -#end if -'ascii' 'summarize_input' -#else: -'${options_type.output_type}' '${options_type.force_quality_encoding}' '${options_type.summarize_input}' -#end if -#if $OptionPairedEnd.pairedEnd == "Yes": -'$OptionPairedEnd.pairedEnd_input' '$output_pairedEndFile' -#else: -'None' 'None' -#end if -</command> - <inputs> - <param name="input_file" type="data" format="txt" label="The File list to groom" /> - <param name="input_type" type="select" label="Input FASTQ quality scores type"> - <option value="solexa">Solexa</option> - <option value="illumina">Illumina 1.3-1.7</option> - <option value="sanger" selected="True">Sanger</option> - <option value="cssanger">Color Space Sanger</option> - </param> - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"> - <!-- no options --> - </when> - <when value="advanced"> - <param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format."> - <option value="solexa">Solexa</option> - <option value="illumina">Illumina 1.3+</option> - <option value="sanger" selected="True">Sanger (recommended)</option> - <option value="cssanger">Color Space Sanger</option> - </param> - <param name="force_quality_encoding" type="select" label="Force Quality Score encoding"> - <option value="None">Use Source Encoding</option> - <option value="ascii" selected="True">ASCII</option> - <option value="decimal">Decimal</option> - </param> - <param name="summarize_input" type="select" label="Summarize input data"> - <option value="summarize_input" selected="True">Summarize Input</option> - <option value="dont_summarize_input">Do not Summarize Input (faster)</option> - </param> - </when> - </conditional> - - <conditional name="OptionPairedEnd"> - <param name="pairedEnd" type="select" label="For paired-end analysis."> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="pairedEnd_input" type="data" format="txt" label="input paired-end files list"/> - </when> - <when value="No"> - </when> - </conditional> - - </inputs> - - <outputs> - <data name="output_file" format="txt"> - </data> - <data format="txt" name="output_pairedEndFile" label="output Paired-end fastq files"> - <filter>(OptionPairedEnd['pairedEnd']=='Yes')</filter> - </data> - </outputs> - <help> -**What it does** - -This tool offers several conversions options relating to the FASTQ format. - -When using *Basic* options, the output will be *sanger* formatted or *cssanger* formatted (when the input is Color Space Sanger). - -When converting, if a quality score falls outside of the target score range, it will be coerced to the closest available value (i.e. the minimum or maximum). - -When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in `Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.`_ - -When converting between color space (csSanger) and base/sequence space (Sanger, Illumina, Solexa) formats, adapter bases are lost or gained; if gained, the base 'G' is used as the adapter. You cannot convert a color space read to base space if there is no adapter present in the color space sequence. Any masked or ambiguous nucleotides in base space will be converted to 'N's when determining color space encoding. - ------ - -**Quality Score Comparison** - -:: - - SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS - ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII - ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX - !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ - | | | | | | - 33 59 64 73 104 126 - - S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads) - I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads) - X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads) - -Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format - -.. class:: infomark - -Output from Illumina 1.8+ pipelines are Sanger encoded. - ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ - - -.. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: http://www.ncbi.nlm.nih.gov/pubmed/20015970 - - </help> -</tool> |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/fastq_groomer_parallel_unSQL.py --- a/SMART/DiffExpAnal/fastq_groomer_parallel_unSQL.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,168 +0,0 @@ -import sys, os, optparse,shutil, random -from commons.core.launcher.Launcher import Launcher -from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory -from commons.core.utils.FileUtils import FileUtils - -def _map(iLauncher, cmd, cmdStart, cmdFinish ): - lCmds = [] - lCmds.extend(cmd) - lCmdStart = [] - lCmdStart.extend(cmdStart) - lCmdFinish = [] - lCmdFinish.extend(cmdFinish) - return(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish)) - -def splitFastQ(fileName, nbOfSeqPerBatch): - nbOfLinesPerFile = nbOfSeqPerBatch * 4 - lOutput = [] - filePrefix, fileExt = os.path.splitext(os.path.basename(fileName)) - resDir = os.path.dirname(fileName) - with open(fileName) as inF: - fileNb = 1 - line = inF.readline() - if not line or nbOfLinesPerFile == 0: - outFileName = "%s/%s-%s%s" %(resDir, filePrefix, fileNb, fileExt) - lOutput.append(outFileName) - f = open(outFileName, "wb") - shutil.copyfileobj(open(fileName, "rb"), f) - f.close() - else: - while line: - outFileName = "%s/%s-%s%s" %(resDir, filePrefix, fileNb, fileExt) - lOutput.append(outFileName) - with open(outFileName, "w") as outF: - lineNb = 1 - while lineNb <= nbOfLinesPerFile and line: - outF.write(line) - line = inF.readline() - lineNb += 1 - fileNb += 1 - return lOutput - -def joinFastQ(dCutOut2Out): - for key in dCutOut2Out.keys(): - FileUtils.catFilesFromList(dCutOut2Out[key],key, False) - -def _createFastqGroomerCode(outGroomerNames, inputFileNames, input_type, output_type, force_quality_encoding, summarize_input): - cmd2Launch = [] - cmd2Launch.append("log = 0") - cmd2Launch.append("from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter") - cmd2Launch.append("aggregator = fastqAggregator()") - cmd2Launch.append("out = fastqWriter( open( '%s', 'wb' ), format = '%s', force_quality_encoding = '%s')" % (outGroomerNames,output_type,force_quality_encoding)) - cmd2Launch.append("read_count = None") - if summarize_input: - cmd2Launch.append("reader = fastqVerboseErrorReader") - else: - cmd2Launch.append("reader = fastqReader") - cmd2Launch.append("for read_count, fastq_read in enumerate( reader( open( '%s' ), format = '%s', apply_galaxy_conventions = True ) ):" % (inputFileNames, input_type)) - if summarize_input: - cmd2Launch.append("\taggregator.consume_read( fastq_read )") - cmd2Launch.append("\tout.write( fastq_read )") - cmd2Launch.append("out.close()") - cmd2Launch.append("if read_count is not None:") - #cmd2Launch.append("\tprint 'Groomed %s %s reads into %s reads.' % ( read_count + 1, %s, %s )" % ('%i', '%s', '%s', input_type,output_type)) - cmd2Launch.append("\tif '%s' != '%s' and 'solexa' in [ '%s', '%s' ]:" % (input_type, output_type, input_type, output_type)) - cmd2Launch.append("\t\tprint 'Converted between Solexa and PHRED scores.'") - if summarize_input: - cmd2Launch.append("\tprint 'Based upon quality and sequence, the input data is valid for: %s' % ( ', '.join( aggregator.get_valid_formats() ) or 'None' )") - cmd2Launch.append("\tascii_range = aggregator.get_ascii_range()") - cmd2Launch.append("\tdecimal_range = aggregator.get_decimal_range()") - cmd2Launch.append("\tprint 'Input ASCII range: %s(%i) - %s(%i)' % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) )") - cmd2Launch.append("\tprint 'Input decimal range: %i - %i' % ( decimal_range[0], decimal_range[1] ) ") - cmd2Launch.append("else:") - cmd2Launch.append("\tprint 'No valid FASTQ reads were provided.'") - cmd2Launch.append("\tlog = 255") - return cmd2Launch - -def stop_err(msg): - sys.stderr.write("%s\n" % msg) - sys.exit() - -def main(): - - input_filename = sys.argv[1] #a txt file - input_type = sys.argv[2] - output_filename = sys.argv[3] #a txt file - output_type = sys.argv[4] - force_quality_encoding = sys.argv[5] - summarize_input = sys.argv[6] == 'summarize_input' - pairedEnd_input = sys.argv[7] - if pairedEnd_input == 'None': - pairedEnd_input = None - else: - output_pairedEndFileName = sys.argv[8] - - if force_quality_encoding == 'None': - force_quality_encoding = None - - #Parse the input txt file and read a list of fastq files - file = open(input_filename, "r") - lines = file.readlines() - inputFileNames = [] - outGroomerNames = [] - resDirName = os.path.dirname(output_filename) + "/" - #Write output txt file and define all output groomer file names - outFile = open(output_filename, "w") - for line in lines: - tab = line.split() - inputFileNames.append(tab[1]) - outGroomerName = resDirName + tab[0] + '_outGroomer_%s.fastq' % random.randrange(0, 10000) - outGroomerNames.append(outGroomerName) - outFile.write(tab[0] + '\t' + outGroomerName + '\n') - outFile.close() - file.close() - - if pairedEnd_input != None: - inPairedFile = open(pairedEnd_input, "r") - lines = inPairedFile.readlines() - inputPairedEndFileNames = [] - outGroomerPairedEndNames = [] - outPairedEndFile = open(output_pairedEndFileName, "w") - for line in lines: - tab = line.split() - inputPairedEndFileNames.append(tab[1]) - outGroomerPairedEndName = resDirName + tab[0] + '_outGroomer_pairedEnd_%s.fastq' % random.randrange(0, 10000) - outGroomerPairedEndNames.append(outGroomerPairedEndName) - outPairedEndFile.write(tab[0] + '\t' + outGroomerPairedEndName + '\n') - outPairedEndFile.close() - inPairedFile.close() - - acronym = "fastqGroomer" - jobdb = TableJobAdaptatorFactory.createJobInstance() - iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True) - lCmdsTuples = [] - dCutOut2Out = {} - lAllFile2remove = [] - # Write output file - for i in range(len(outGroomerNames)): - lCutInputFile = splitFastQ(inputFileNames[i], 20000) - lAllFile2remove.extend(lCutInputFile) - lCutOutput = [] - for cutInput in lCutInputFile: - cutOutput = "%s_out" % cutInput - lCutOutput.append(cutOutput) - lAllFile2remove.extend(lCutOutput) - cmd2Launch = _createFastqGroomerCode(cutOutput, cutInput, input_type, output_type, force_quality_encoding, summarize_input) - cmdStart = [] - cmdFinish = [] - lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish)) - dCutOut2Out[outGroomerNames[i]] = lCutOutput - if pairedEnd_input != None: - lCutInputFile = splitFastQ(inputPairedEndFileNames[i], 20000) - lAllFile2remove.extend(lCutInputFile) - lCutOutput = [] - for cutInput in lCutInputFile: - cutOutput = "%s_out" % cutInput - lCutOutput.append(cutOutput) - lAllFile2remove.extend(lCutOutput) - cmd2Launch = _createFastqGroomerCode(cutOutput, cutInput, input_type, output_type, force_quality_encoding, summarize_input) - cmdStart = [] - cmdFinish = [] - lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish)) - dCutOut2Out[outGroomerPairedEndNames[i]] = lCutOutput - iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, False) - - joinFastQ(dCutOut2Out) - FileUtils.removeFilesFromListIfExist(lAllFile2remove) - -if __name__ == "__main__": main() |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/fastq_groomer_parallel_unSQL.xml --- a/SMART/DiffExpAnal/fastq_groomer_parallel_unSQL.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,122 +0,0 @@ -<tool id="fastq_groomer_parallel_unSQL" name="FASTQ Groomer (for DEA in parallel)" version="1.0.0"> - <description>convert between various FASTQ quality formats for a list of inputs (parallelized).</description> - <command interpreter="python">fastq_groomer_parallel_unSQL.py '$input_file' '$input_type' '$output_file' -#if str( $options_type['options_type_selector'] ) == 'basic': -#if str( $input_type ) == 'cssanger': -'cssanger' -#else: -'sanger' -#end if -'ascii' 'summarize_input' -#else: -'${options_type.output_type}' '${options_type.force_quality_encoding}' '${options_type.summarize_input}' -#end if -#if $OptionPairedEnd.pairedEnd == "Yes": -'$OptionPairedEnd.pairedEnd_input' '$output_pairedEndFile' -#else: -'None' 'None' -#end if -</command> - <inputs> - <param name="input_file" type="data" format="txt" label="The File list to groom" /> - <param name="input_type" type="select" label="Input FASTQ quality scores type"> - <option value="solexa">Solexa</option> - <option value="illumina">Illumina 1.3-1.7</option> - <option value="sanger" selected="True">Sanger</option> - <option value="cssanger">Color Space Sanger</option> - </param> - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"> - <!-- no options --> - </when> - <when value="advanced"> - <param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format."> - <option value="solexa">Solexa</option> - <option value="illumina">Illumina 1.3+</option> - <option value="sanger" selected="True">Sanger (recommended)</option> - <option value="cssanger">Color Space Sanger</option> - </param> - <param name="force_quality_encoding" type="select" label="Force Quality Score encoding"> - <option value="None">Use Source Encoding</option> - <option value="ascii" selected="True">ASCII</option> - <option value="decimal">Decimal</option> - </param> - <param name="summarize_input" type="select" label="Summarize input data"> - <option value="summarize_input" selected="True">Summarize Input</option> - <option value="dont_summarize_input">Do not Summarize Input (faster)</option> - </param> - </when> - </conditional> - - <conditional name="OptionPairedEnd"> - <param name="pairedEnd" type="select" label="For paired-end analysis."> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="pairedEnd_input" type="data" format="txt" label="input paired-end files list"/> - </when> - <when value="No"> - </when> - </conditional> - - </inputs> - - <outputs> - <data name="output_file" format="txt"> - </data> - <data format="txt" name="output_pairedEndFile" label="output Paired-end fastq files"> - <filter>(OptionPairedEnd['pairedEnd']=='Yes')</filter> - </data> - </outputs> - <help> -**What it does** - -This tool offers several conversions options relating to the FASTQ format. - -When using *Basic* options, the output will be *sanger* formatted or *cssanger* formatted (when the input is Color Space Sanger). - -When converting, if a quality score falls outside of the target score range, it will be coerced to the closest available value (i.e. the minimum or maximum). - -When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in `Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.`_ - -When converting between color space (csSanger) and base/sequence space (Sanger, Illumina, Solexa) formats, adapter bases are lost or gained; if gained, the base 'G' is used as the adapter. You cannot convert a color space read to base space if there is no adapter present in the color space sequence. Any masked or ambiguous nucleotides in base space will be converted to 'N's when determining color space encoding. - ------ - -**Quality Score Comparison** - -:: - - SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS - ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII - ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX - !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ - | | | | | | - 33 59 64 73 104 126 - - S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads) - I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads) - X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads) - -Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format - -.. class:: infomark - -Output from Illumina 1.8+ pipelines are Sanger encoded. - ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ - - -.. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: http://www.ncbi.nlm.nih.gov/pubmed/20015970 - - </help> -</tool> |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/gsnap.xml --- a/SMART/DiffExpAnal/gsnap.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,42 +0,0 @@ -<tool id="gsnap" name="gsnap"> - - <description>GSNAP version 2012-12-20. - GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and - GSNAP: Genomic Short-read Nucleotide Alignment Program - </description> - - <command interpreter="python"> wrappGSNAP.py - -d $genomeName -i $inputFasta -k $kmer -q $inputFastq -A $outputFormat -o $outputSam - - #if $optionPairedEnd.paire == 'Yes': - -p $optionPairedEnd.pairedEndFile - #end if - - </command> - - <inputs> - <param name="inputFasta" type="data" format="fasta" label="Reference genome file, fasta format."/> - <param name="genomeName" type="text" value="Arabidopsis_Thaliana" label="Please give the reference genome a name! (Ex. Arabidopsis_Thaliana)"/> - <param name="kmer" type="integer" value="12" label="Choose kmer value (superior or egal at 16), a big kmer value can take more RAM(4Go)." /> - <param name="inputFastq" type="data" format="fastq" label="Input fastq file."/> - <param name="outputFormat" type="text" format="sam" label="Choose an output format [sam, goby (need to re-compile with appropriate options)]."/> - - <conditional name="optionPairedEnd"> - <param name="paire" type="select" label="pairedEnd fastq file"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="pairedEndFile" type="data" format="fastq"/> - </when> - <when value="No"> - </when> - </conditional> - - </inputs> - - <outputs> - <data format="sam" name="outputSam" label="gsnap Output"/> - </outputs> - -</tool> |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/gsnap_parallel_unSQL.py --- a/SMART/DiffExpAnal/gsnap_parallel_unSQL.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,195 +0,0 @@\n-#!/usr/bin/env python\n-\n-import optparse, os, shutil, subprocess, sys, tempfile, fileinput, tarfile, glob \n-import time\n-from commons.core.launcher.Launcher import Launcher\n-from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory\n-from commons.core.utils.FileUtils import FileUtils\n-from optparse import OptionParser\n-\n-def stop_err( msg ):\n- sys.stderr.write( "%s\\n" % msg )\n- sys.exit()\n-\n-def toTar(tarFileName, accepted_hits_outputNames):\n- tfile = tarfile.open(tarFileName + ".tmp.tar", "w")\n- currentPath = os.getcwd()\n- os.chdir(dir)\n- for file in accepted_hits_outputNames:\n- relativeFileName = os.path.basename(file)\n- tfile.add(relativeFileName)\n- os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))\n- tfile.close()\n- os.chdir(currentPath)\n- \n-def joinSAM(dCutOut2Out):\n- for key in dCutOut2Out.keys():\n- FileUtils.catFilesFromList(dCutOut2Out[key],key, False)\n- \n-def _map(iLauncher, cmd, cmdStart, cmdFinish ):\n- lCmds = []\n- lCmds.extend(cmd)\n- lCmdStart = []\n- lCmdStart.extend(cmdStart)\n- lCmdFinish = []\n- lCmdFinish.extend(cmdFinish)\n- return(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))\n-\n-def _createGsnapSplicingOptions(options):\n- lArgs = []\n- lArgs.append("-N %s" % options.novelsplicing)\n- if options.useSplicing:\n- lArgs.append("-s %s" % options.useSplicing)\n- lArgs.append("-w %s" % options.localsplicedist)\n- lArgs.append("-e %s" % options.localSplicePenality)\n- lArgs.append("-E %s" % options.distantSplicePenality)\n- lArgs.append("-K %s" % options.distantSpliceEndlength)\n- lArgs.append("-l %s" % options.shortendSpliceEndlength)\n- \n- \n- return lArgs\n-\n-def _createGsnapPairedEndOptions(options):\n- lArgs = []\n- if not(options.useSplicing or options.pairedEndFile):\n- lArgs.append("--pairmax-dna %s" % options.pairmaxRna)\n- if options.useSplicing or options.pairedEndFile:\n- lArgs.append("--pairmax-rna %s" % options.pairmaxRna)\n- lArgs.append("--pairexpect=%s" % options.pairexpect)\n- lArgs.append("--pairdev=%s" % options.pairedev)\n- \n- \n-\n-def _createGsnapCommand(iLauncher, options, workingDir, inputFileNames, inputRevFilesNames, outputFileName, batchNumber, numberOfBatch):\n- lArgs = []\n- lArgs.append("-d %s" % options.genomeName)\n- lArgs.append("-k %s" % options.kmer)\n- lArgs.append("-D %s" % workingDir)\n- lArgs.append("-A %s" % options.outputFormat)\n- lArgs.append("-q %s/%s" % (batchNumber, numberOfBatch))\n- lArgs.append("--no-sam-headers")\n- lArgs.append(inputFileNames)\n- print \'N option: %s, pairedEndFile option: %s\' %(options.novelsplicing, options.pairedEndFile)\n- if options.pairedEndFile:\n- lArgs.append(inputRevFilesNames)\n- if options.novelsplicing == \'1\':\n- lArgs.extend(_createGsnapSplicingOptions(options))\n- elif options.pairedEndFile:\n- lArgs.extend(_createGsnapPairedEndOptions(options))\n- \n- lArgs.append("> %s" % outputFileName) \n- return iLauncher.getSystemCommand("gsnap", lArgs) \n-\n-def __main__():\n- #Parse Command Line\n- description = "GMAP/GSNAP version:2012-12-20."\n- parser = OptionParser(description = description)\n- parser.add_option(\'-o\', \'--outputTxtFile\', dest=\'outputTxtFile\', help=\'for Differential expression analysis pipeline, new output option gives a txt output containing the list of mapping results.\')\n- parser.add_option("-q", "--inputTxt", dest="inputTxt", action="store", type="string", help="input, a txt file for a list of input reads files [compulsory]")\n- parser.add_option(\'-t\', \'--tar\', dest=\'outputTar\', default=None, help=\'output all accepted hits results in a tar file.\' )\n- parser.add_option("-d", "--genomeName", dest="genomeName", help="Define the reference genome name.[compulsory]")\n-# parser.add_option("-o", "--outputFile", dest='..b'h for RNA-Seq paired reads, or other reads that could have a splice (default 200000).")\n- parser.add_option("--pairexpect", dest="pairexpect", default=200, help="Expected paired-end length, used for calling splices in medial part of paired-end reads (default 200)")\n- parser.add_option("--pairdev", dest="pairdev", default=25, help="Allowable deviation from expected paired-end length, used for calling splices in medial part of paired-end reads (default 25)")\n- \n- (options, args) = parser.parse_args() \n-\n- workingDir = os.path.dirname(options.inputFastaFile)\n- \n- file = open(options.inputTxt,"r")\n- lines = file.readlines()\n- inputFileNames = []\n- gsnapOutputNames = []\n- outputName = options.outputTxtFile\n- resDirName = os.path.dirname(outputName) + \'/\'\n- out = open(outputName, "w")\n- for line in lines:\n- timeId = time.strftime("%Y%m%d%H%M%S")\n- tab = line.split()\n- inputFileNames.append(tab[1])\n- OutputName = resDirName + tab[0] + \'_samOutput_%s.sam\' % timeId\n- gsnapOutputNames.append(OutputName) \n- out.write(tab[0] + \'\\t\' + OutputName + \'\\n\')\n- file.close()\n- out.close()\n- \n- if options.pairedEndFile:\n- revFile = open(options.pairedEndFile,"r")\n- lines = revFile.readlines()\n- inputRevFileNames = []\n- for line in lines:\n- revTab = line.split()\n- inputRevFileNames.append(revTab[1])\n- revFile.close()\n-\n- #Create gsnap make \n- lCmdsTuples =[]\n- acronym = "gsnap_make"\n- jobdb = TableJobAdaptatorFactory.createJobInstance()\n- iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True)\n- cmds = []\n- cmd_setup = "gmap_setup -d %s -D %s -k %s %s;" % (options.genomeName, workingDir, options.kmer, options.inputFastaFile)\n- cmds.append(cmd_setup)\n- cmd_make_coords = "make -f Makefile.%s coords;" % options.genomeName \n- cmds.append(cmd_make_coords)\n- cmd_make_gmapdb = "make -f Makefile.%s gmapdb;" % options.genomeName\n- cmds.append(cmd_make_gmapdb)\n- cmd_make_install = "make -f Makefile.%s install;" % options.genomeName\n- cmds.append(cmd_make_install)\n- cmd_index = iLauncher.getSystemCommand("", cmds)\n- cmd2Launch = []\n- cmdStart = []\n- cmdFinish = []\n- cmd2Launch.append(cmd_index)\n- lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish)) \n- iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True) \n- \n- acronym = "gsnap"\n- jobdb = TableJobAdaptatorFactory.createJobInstance()\n- iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True)\n- lCmdsTuples = []\n- dCutOut2Out = {}\n- lAllFile2remove = []\n- numberOfBatch = 20 #usually for testing, working on to find a value for default launch on galaxy\n- for i in range(len(inputFileNames)):\n- lCutOutput = []\n- for j in range(numberOfBatch):\n- cutOutput = "%s_out_%s" % (inputFileNames[i], j)\n- lCutOutput.append(cutOutput)\n- lAllFile2remove.extend(lCutOutput)\n- cmd2Launch = []\n- if options.pairedEndFile: \n- inputRevFile = inputRevFileNames[i]\n- else:\n- inputRevFile = ""\n- cmd2Launch.append(_createGsnapCommand(iLauncher, options, workingDir, inputFileNames[i], inputRevFile, cutOutput, j, numberOfBatch))\n- cmdStart = []\n- cmdFinish = []\n- lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish)) \n- dCutOut2Out[gsnapOutputNames[i]] = lCutOutput\n- iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True)\n- \n- joinSAM(dCutOut2Out) \n- FileUtils.removeFilesFromListIfExist(lAllFile2remove) \n- \n- if options.outputTar != None:\n- toTar(options.outputTar, gsnapOutputNames)\n-\n-\n-if __name__=="__main__": __main__()\n' |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/gsnap_parallel_unSQL.xml --- a/SMART/DiffExpAnal/gsnap_parallel_unSQL.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,46 +0,0 @@ -<tool id="gsnap_parallel_unSQL" name="GSNAP (for DEA in parallel)" version="1.0.0"> - <description>Genomic Short-read Nucleotide Alignment Program in parallel for Differential Expression Analysis (DEA)</description> - <command interpreter="python">gsnap_parallel_unSQL.py - -i $genome_file - -q $fastq_file_list - -o $output_file_list - -d $genome_prefix - -k $kmer_size - #if $OptionPairedEnd.pairedEnd == 'Yes': - -p $pairedEnd_input - #end if - -</command> - <inputs> - <param name="genome_file" type="data" format="fasta" label="Genome fasta file" /> - <param name="fastq_file_list" type="data" format="txt" label="Fastq file list" /> - <param name="genome_prefix" type="text" format="txt" label="Prefix used to name genome index " /> - <param name="kmer_size" type="integer" value="12" label="Kmer size"/> - - <conditional name="OptionPairedEnd"> - <param name="pairedEnd" type="select" label="For paired-end analysis."> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="pairedEnd_input" type="data" format="txt" label="input paired-end files list"/> - </when> - <when value="No"> - </when> - </conditional> - - </inputs> - - <outputs> - <data name="output_file_list" format="txt"/> - </outputs> - <help> -**What it does** - -To complete - -**Citation** - -If you use this tool, please cite "Thomas D. Wu and Serban Nacu, Fast and SNP-tolerant detection of complex variants and splicing in short reads, Bioinformatics 2010 26:873-881" - </help> -</tool> |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/listInputs.pl --- a/SMART/DiffExpAnal/listInputs.pl Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,13 +0,0 @@ -#!/usr/bin/perl -w - -use strict; - -my $in_file1 = $ARGV[0]; -my $in_file2 = $ARGV[1]; -my $out_file = $ARGV[2]; - -open(OUT, ">$out_file"); -print OUT "label\tfiles\tgroup\n"; -print OUT "fileID=1\t$in_file1\tgroup1\n"; -print OUT "fileID=2\t$in_file2\tgroup2\n"; -close(OUT); |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/listInputs.xml --- a/SMART/DiffExpAnal/listInputs.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,25 +0,0 @@ -<tool id="listInputs" name="listInputs"> - <description>Give a list of input files from different conditions/groups for DESeq analysis, DESeq can then charge these input files from the given list.</description> - <command interpreter="perl"> listInputs.pl $inputFromGroup1 $inputFromGroup2 $output - </command> - - <inputs> - <param name="inputFromGroup1" type="data" format="tabular" label="Please choose your file from group1."/> - <param name="inputFromGroup2" type="data" format="tabular" label="Please choose your file from group2."/> - </inputs> - - <outputs> - <data format="txt" name="output" label="listInputs Output"/> - </outputs> - - <help> - This tool can facilate the the chargement for DESeq tool. - Example: - From group1, we have input1. - From group2, we have input2. - This tool will give us a list like: - fileID=1 input1 group1 - fileID=2 input2 group2 - Where the value of fileID is unique for each input file. - </help> -</tool> |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/loadHTSeqResultFiles.py --- a/SMART/DiffExpAnal/loadHTSeqResultFiles.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -import optparse, sys - - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option('-i', '--inputs', dest='inputFiles', default=None, help='several input files. (seperated by @ or @@' ) - parser.add_option( '-o', '--output', dest='outputFile', default=None, help='The output list of HTSeq results files(.tabular) on txt format.' ) - ( options, args ) = parser.parse_args() - - - out = open(options.outputFile, 'w') - out.write("label\tfiles\tgroup\n") - if options.inputFiles == None: - raise Exception, 'input file name is not defined!' - - groupCount = 1 - fileCount = 0 - - inputFiles = sys.argv[6:] - print '\n\nthe length of inputfiles is : %s \n' % len(inputFiles) - i = 0 - while i < (len(inputFiles)-1): - if inputFiles[i] == "@": - i += 1 - fileCount = 1 - groupCount += 1 - out.write("Group%s_%s\t%s\t%s\n" % (groupCount, fileCount, inputFiles[i], groupCount)) - else: - fileCount += 1 - out.write("Group%s_%s\t%s\t%s\n" % (groupCount, fileCount, inputFiles[i], groupCount)) - i += 1 - - out.close() - - - -if __name__=="__main__": __main__() |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/loadHTSeqResultFiles.xml --- a/SMART/DiffExpAnal/loadHTSeqResultFiles.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,29 +0,0 @@ -<tool id="load_HTSeqResultFiles" name="load HTSeqResultFiles" > - <description>To load several HTSeq result files from different conditions.</description> - <command interpreter="python"> loadHTSeqResultFiles.py -o $htseqRes_out - -i - #for $i in $condition_groups - #for $j in $i.replicates - $j.tabular_file - #end for - @ - #end for - -</command> - <inputs> - <repeat name="condition_groups" title="Condition group" min="2"> - <repeat name="replicates" title="Replicate"> - <param name="tabular_file" format="tabular" type="data" label="TABULAR file."/> - </repeat> - </repeat> - </inputs> - - <outputs> - <data format="txt" name="htseqRes_out" label="HTSeq result files" help="This program gives you a list of files you choose for the following data analysis."/> - -</outputs> -<help> -</help> - -</tool> - |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/loadMultiFastqFiles.py --- a/SMART/DiffExpAnal/loadMultiFastqFiles.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,70 +0,0 @@ -#!/usr/bin/env python - -import optparse, sys - - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option('-i', '--inputs', dest='inputFiles', default=None, help='several input files. (seperated by @ or @@' ) - parser.add_option( '-o', '--output', dest='outputSingleFile', default=None, help='The output list of fastq files on txt format.' ) - parser.add_option( '', '--pairedEnd', dest='outputPaireFile', default=None, help='paired end option help to upload the corresponding paired end complementary fastq files' ) - ( options, args ) = parser.parse_args() - - - - if options.outputSingleFile == None: - raise Exception, 'OutSingleFile txt file name is not defined!' - else: - outSingle = open(options.outputSingleFile, 'w') - - if options.inputFiles == None: - raise Exception, 'input file name is not defined!' - - groupCount = 1 - fileCount = 0 - - if options.outputPaireFile == None: - inputFiles = sys.argv[4:] - i = 0 - while i < (len(inputFiles)-1): - if inputFiles[i] == "@": - i += 1 - fileCount = 1 - groupCount += 1 - outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i])) - - else: - fileCount += 1 - outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i])) - - i += 1 - else: - inputFiles = sys.argv[6:] - print '\n\nthe length of inputfiles is : %s \n' % len(inputFiles) - outPaire = open(options.outputPaireFile, 'w') - i = 0 - while i < (len(inputFiles)-1): - if inputFiles[i] == "@@": - i += 1 - outPaire.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i])) - elif inputFiles[i] == "@": - i += 1 - fileCount = 1 - groupCount += 1 - outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i])) - else: - fileCount += 1 - outSingle.write("Group%s_%s\t%s\n" % (groupCount, fileCount, inputFiles[i])) - - i += 1 - - - - outPaire.close() - - outSingle.close() - - - -if __name__=="__main__": __main__() |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/loadMultiFastqFiles.sh --- a/SMART/DiffExpAnal/loadMultiFastqFiles.sh Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,24 +0,0 @@ -#!/bin/bash - -OUTFile=${1} -shift -groupCount=1 -replicateNumber=1 - -arrayZ=( $@ ) -#remove the last symble '@' given by commande line -unset arrayZ[${#arrayZ[@]}-1] - -for FILE in ${arrayZ[@]} -do - #if a new group of fastq, re-count the replicateNumber - if echo $FILE | grep -q "@" - then - groupCount=$(($groupCount + 1)) - replicateNumber=1 - else - echo -e "Group${groupCount}_${replicateNumber}\t${FILE}" >>${OUTFile} - replicateNumber=$(($replicateNumber + 1)) - fi -done - |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/loadMultiFastqFiles.xml --- a/SMART/DiffExpAnal/loadMultiFastqFiles.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,75 +0,0 @@ -<tool id="load_multiFASTQFiles" name="load_multiFASTQfiles" > - <description>To load several FASTQ files from different conditions.</description> - <command interpreter="python"> loadMultiFastqFiles.py -o $multiFASTQfiles_out -#if $single_end_paired_end.mapping_mode == 'single': - -i - #for $i in $single_end_paired_end.condition_groups - #for $j in $i.replicates - $j.fastq_file - #end for - @ - #end for - -#elif $single_end_paired_end.mapping_mode == 'paired': - - --pairedEnd $multiFASTQfiles_paired_end_out - -i - #for $i in $single_end_paired_end.condition_groups - #for $j in $i.replicates - $j.fastq_file - @@ - $j.fastq_paired_end_file - #end for - @ - #end for -#end if - -</command> - <inputs> - <conditional name="single_end_paired_end"> - <param name="mapping_mode" type="select" label="The uploading fastq files for single-end or paired-end mapping mode."> - <option value="single">Single-End</option> - <option value="paired">Paire-End</option> - </param> - <when value="single"> - <repeat name="condition_groups" title="Condition group" min="2"> - <repeat name="replicates" title="Replicate"> - <param name="fastq_file" format="fastq" type="data" label="FASTQ file. Can show the sequences quality."/> - </repeat> - </repeat> - </when> - <when value="paired"> - <repeat name="condition_groups" title="Condition group" min="2"> - <repeat name="replicates" title="Replicate"> - <param name="fastq_file" format="fastq" type="data" label="FASTQ file. Can show the sequences quality."/> - <param name="fastq_paired_end_file" format="fastq" type="data" label="fastq paired end complementary file" help="Add the corresponding paired end file for paired end mapping"/> - </repeat> - </repeat> - </when> - - </conditional> - </inputs> - - <outputs> - <data format="txt" name="multiFASTQfiles_out" label="loadMultiFASTQFiles result" help="This program gives you a list of files you choose for the following data analysis."/> - <data format="txt" name="multiFASTQfiles_paired_end_out" label="loadMultiFASTQFiles for paired end result" help="This program gives you a list of files you choose for the following data analysis."> - <filter>(single_end_paired_end['mapping_mode']=='paired')</filter> - - </data> -</outputs> -<help> - **This tool is to help upload several data for differential expression pipeline. Before click 'Execute', you should Click** Ctrl + here_ **first to open the pipeline in a new page.** - - .. _here: http://127.0.0.1:8085/u/yufei-luo/w/differentialexpressiondeseq-with-replicates -</help> - -</tool> - - - - - - - - - |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/testR.R --- a/SMART/DiffExpAnal/testR.R Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,93 +0,0 @@ -#!/usr/bin - -library(DESeq) -library(hexbin) -library(latticeExtra) -library(gplots) -library(geneplotter) -library(Biobase) - -##In a file called test_args.R -args <- commandArgs() - - -fileName <- args[4] -colNames <- as.integer(unlist(strsplit(args[5], ","))) -colCond1 <- as.integer(unlist(strsplit(args[6], ","))) -colCond2 <- as.integer(unlist(strsplit(args[7], ","))) -OUTPUTCSV <- args[8] -OUTPUTPNG <- args[9] - -if(colNames[1]!=0){ - countsTable <- read.delim(fileName, row.names=1) - conditions <- c((colNames[length(colNames)]+1):ncol(countsTable)) -} else if(colNames[1]==0){ - countsTable <- read.delim(fileName) - conditions <- c(1:ncol(countsTable)) - rownames(countsTable) <- paste( "Gene", 1:nrow(countsTable), sep="_" )} - -for(i in colCond1){conditions[i] = "A"} -for(i in colCond2){conditions[i] = "B"} -conditions -#analysis with DESeq -cds <- newCountDataSet( countsTable, conditions ) -cds <- estimateSizeFactors( cds ) -cds <- estimateVarianceFunctions( cds ) -result <- nbinomTest( cds, "A", "B" ) -#stock the result dans un .tsv as output file -write.table(result, OUTPUTCSV, sep = " ", quote = FALSE, col.names = NA) - -#figures for DE analysis -#pdf( OUTPUTPNG, width=4, height=4 ) -png( filename=OUTPUTPNG, width=700, height=700 ) -#png format is not as clear as pdf format!!!!!!!!!!!!!!!!!!!!!!!!! -print(xyplot( - log2FoldChange ~ I(baseMean), - result, - pch=16, cex=.3, - col=ifelse(result$padj < .1, "#FF000040","#00000040" ), - panel = function( x, y, col, ...) { - above <- (y > 5.8) - below <- (y < -5.8) - inside <- !( above | below ) - panel.xyplot( x=x[inside], y=y[inside], col=col[inside], ...) - panel.arrows( x[above], 5.8, x[above], 5.95, col=col[above],length=".1", unit="native" ) - panel.arrows( x[below], -5.8, x[below], -5.95, col=col[below],length=".1", unit="native" ) }, - axis = function(side, ...) { - if( side=="left") { - panel.axis( side, outside=TRUE, at=seq(-14,14,by=1), labels=FALSE ) - panel.axis( side, outside=TRUE, at=seq(-10,10,by=5), labels=TRUE ) - } - if( side=="bottom") { - panel.axis( side, outside=TRUE, at=seq(-2,10,by=1), rot=0, - labels = do.call( expression, - lapply( seq(-2,10,by=1), function(a) - substitute( 10^b, list(b=a) ) ) ) ) - } }, - xlab = "mean", ylab = "log2 fold change", - scales = list(x = list( log=TRUE ),y = list( log=FALSE, limits=c( -6, 6 ) ) ) )) -dev.off() - -#The volcano plot -#pdf( "vulcano_fly.pdf", width=4, height=4 ) -#print(xyplot( -log10( pval ) ~ log2FoldChange, -# result, -# pch=20, cex=.2, -# col=ifelse( result$padj<.1, "#FF000050", "#00000050" ), -# axis = function( side, ... ) { -# if( side=="bottom") { -# panel.axis( side, outside=TRUE, at=seq(-14,14,by=1), labels=FALSE ) -# panel.axis( side, outside=TRUE, at=seq(-10,10,by=5), labels=TRUE ) -# } -# if( side=="left") { -# panel.axis( side, outside=TRUE, at=seq(0,25,by=1), labels=FALSE ) -# panel.axis( side, outside=TRUE, at=seq(0,25,by=5), -# labels = do.call( expression, -# lapply( seq(0,25,by=5), function(a) -# substitute( 10^-b, list(b=a) ) ) ) ) -# } }, -# xlab = "log2 fold change", ylab = "p value", -# scales = list( -# x = list( limits=c( -6, 6 ) ), -# y = list( limits=c( 0, 25 ) ) ) )) -#dev.off() |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/testR.sh --- a/SMART/DiffExpAnal/testR.sh Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,11 +0,0 @@ -#! /bin/sh - -#cat testR.R | R --slave --args $1 $2 $3 $4 $5 $6 < DiffExpAnal/testR.R - -#ex1. sh testR.sh fly_RNA_counts.tsv 0 1,3 2,4 output_fly.csv output_fly.png -#ex2. sh testR.sh NeuralStemCellData.tab 1 2,3,4 5,6 output_modif.csv output_modif.png - -#cat /share/apps/galaxy-dist/tools/repet_pipe/SMART/DiffExpAnal/testR.R | R --slave --args $1 $2 $3 $4 $5 $6 < /share/apps/galaxy-dist/tools/repet_pipe/SMART/DiffExpAnal/testR.R - -#$1=targetFile(the list of files) $2=with or without replicate -cat /share/apps/galaxy-dist/tools/repet_pipe/SMART/DiffExpAnal/DESeqTools/anadiffGenes2conds.R| R --slave --args $1 $2 < /share/apps/galaxy-dist/tools/repet_pipe/SMART/DiffExpAnal/DESeqTools/anadiffGenes2conds.R |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/tophat_parallel.py --- a/SMART/DiffExpAnal/tophat_parallel.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,325 +0,0 @@\n-\n-#!/usr/bin/env python\n-\n-import optparse, os, shutil, subprocess, sys, tempfile, fileinput, tarfile,random\n-\n-def stop_err( msg ):\n- sys.stderr.write( "%s\\n" % msg )\n- sys.exit()\n-\n-def toTar(tarFileName, accepted_hits_outputNames):\n- fileName = os.path.splitext(tarFileName)[0]\n- fileNameBaseName = os.path.basename(fileName)\n- dir = os.path.dirname(tarFileName) \n- tfile = tarfile.open(tarFileName + ".tmp.tar", "w")\n- currentPath = os.getcwd()\n- os.chdir(dir)\n- for file in accepted_hits_outputNames:\n- relativeFileName = os.path.basename(file)\n- tfile.add(relativeFileName)\n- os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))\n- tfile.close()\n- os.chdir(currentPath)\n- \n-\n-def __main__():\n- #Parse Command Line\n- parser = optparse.OptionParser()\n- parser.add_option(\'-o\', \'--outputTxtFile\', dest=\'outputTxtFile\', help=\'for Differential expression analysis pipeline, new output option gives a txt output containing the list of mapping results.\')\n- parser.add_option(\'-t\', \'--tar\', dest=\'outputTar\', default=None, help=\'output all accepted hits results in a tar file.\' )\n- parser.add_option( \'-p\', \'--num-threads\', dest=\'num_threads\', help=\'Use this many threads to align reads. The default is 1.\' )\n- parser.add_option( \'-C\', \'--color-space\', dest=\'color_space\', action=\'store_true\', help=\'This indicates color-space data\' )\n- parser.add_option( \'-J\', \'--junctions-output\', dest=\'junctions_output_file\', default=\'junctions_output.bed\', help=\'Junctions output file; formate is BED.\' )\n- parser.add_option( \'-H\', \'--hits-output\', dest=\'accepted_hits_output_file\', default=\'hits_output_%s.bam\' % random.randrange(0, 10000), help=\'Accepted hits output file; formate is BAM.\' )\n- parser.add_option( \'\', \'--own-file\', dest=\'own_file\', help=\'\' )\n- parser.add_option( \'-D\', \'--indexes-path\', dest=\'index_path\', help=\'Indexes directory; location of .ebwt and .fa files.\' )\n- parser.add_option( \'-r\', \'--mate-inner-dist\', dest=\'mate_inner_dist\', help=\'This is the expected (mean) inner distance between mate pairs. \\\n- For, example, for paired end runs with fragments selected at 300bp, \\\n- where each end is 50bp, you should set -r to be 200. There is no default, \\\n- and this parameter is required for paired end runs.\')\n- parser.add_option( \'\', \'--mate-std-dev\', dest=\'mate_std_dev\', help=\'Standard deviation of distribution on inner distances between male pairs.\' )\n- parser.add_option( \'-a\', \'--min-anchor-length\', dest=\'min_anchor_length\', \n- help=\'The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.\' )\n- parser.add_option( \'-m\', \'--splice-mismatches\', dest=\'splice_mismatches\', help=\'The maximum number of mismatches that can appear in the anchor region of a spliced alignment.\' )\n- parser.add_option( \'-i\', \'--min-intron-length\', dest=\'min_intron_length\', \n- help=\'The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart.\' )\n- parser.add_option( \'-I\', \'--max-intron-length\', dest=\'max_intron_length\', \n- help=\'The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.\' )\n- parser.add_option( \'-F\', \'--junction_filter\', dest=\'junction_filter\', help=\'Filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)\' )\n- parser.add_option( \'-g\', \'--max_multihits\', dest=\'max_multihits\', help=\'Maximum number of alignmen'..b'overage-search --min-coverage-intron %s --max-coverage-intron %s \' % ( options.min_coverage_intron, options.max_coverage_intron )\n- else:\n- opts += \'--no-coverage-search \'\n- if options.closure_search:\n- opts += \'--closure-search --min-closure-exon %s --min-closure-intron %s --max-closure-intron %s \' % ( options.min_closure_exon, options.min_closure_intron, options.max_closure_intron ) \n- else:\n- opts += \'--no-closure-search \'\n- if options.microexon_search:\n- opts += \'--microexon-search \'\n- if options.single_paired == \'paired\':\n- opts += \'--mate-std-dev %s \' % options.mate_std_dev\n- if options.initial_read_mismatches:\n- opts += \'--initial-read-mismatches %d \' % int( options.initial_read_mismatches )\n- if options.seg_mismatches:\n- opts += \'--segment-mismatches %d \' % int( options.seg_mismatches )\n- if options.seg_length:\n- opts += \'--segment-length %d \' % int( options.seg_length )\n- if options.min_segment_intron:\n- opts += \'--min-segment-intron %d \' % int( options.min_segment_intron )\n- if options.max_segment_intron:\n- opts += \'--max-segment-intron %d \' % int( options.max_segment_intron )\n- if options.own_file:\n- cmd = cmd % ( opts, index_paths[0], input_files ) #here to add paired end file\n- else:\n- cmd = cmd % ( opts, index_paths[i], input_files ) #here to add paired end file\n- except Exception, e:\n- # Clean up temp dirs\n- if os.path.exists( tmp_index_dir ):\n- shutil.rmtree( tmp_index_dir )\n- stop_err( \'Something is wrong with the alignment parameters and the alignment could not be run\\n\' + str( e ) )\n- \n- cmds.append(cmd)\n-\n- # Run the command line for each file.\n- for i in range(len(cmds)):\n- try:\n- tmp_out = tempfile.NamedTemporaryFile().name\n- tmp_files.append(tmp_out)\n- tmp_stdout = open( tmp_out, \'wb\' )\n- tmp_err = tempfile.NamedTemporaryFile().name\n- tmp_files.append(tmp_err)\n- tmp_stderr = open( tmp_err, \'wb\' )\n- proc = subprocess.Popen( args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )\n- returncode = proc.wait()\n- tmp_stderr.close()\n- # get stderr, allowing for case where it\'s very large\n- tmp_stderr = open( tmp_err, \'rb\' )\n- stderr = \'\'\n- buffsize = 1048576\n- try:\n- while True:\n- stderr += tmp_stderr.read( buffsize )\n- if not stderr or len( stderr ) % buffsize != 0:\n- break\n- except OverflowError:\n- pass\n- tmp_stdout.close()\n- tmp_stderr.close()\n- if returncode != 0:\n- raise Exception, stderr\n- \n- # Copy output files from tmp directory to specified files.\n- #shutil.copyfile( os.path.join( "tophat_out", "junctions.bed" ), junctions_outputNames[i] )\n- shutil.copyfile( os.path.join( "tophat_out", "accepted_hits.bam" ), accepted_hits_outputNames[i] )\n- # TODO: look for errors in program output.\n- except Exception, e:\n- stop_err( \'Error in tophat:\\n\' + str( e ) ) \n-\n- if options.outputTar != None:\n- toTar(options.outputTar, accepted_hits_outputNames)\n-\n- \n- # Clean up temp dirs\n- for tmp_index_dir in tmp_index_dirs:\n- if os.path.exists( tmp_index_dir ):\n- shutil.rmtree( tmp_index_dir )\n-\n- for tmp in tmp_files:\n- os.remove(tmp)\n-\n-\n-if __name__=="__main__": __main__()\n' |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/tophat_parallel.xml --- a/SMART/DiffExpAnal/tophat_parallel.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,577 +0,0 @@\n-<tool id="tophat_parallel" name="Tophat for Illumina (for DEA)" version="1.0.0">\n- <description>Find splice junctions using RNA-seq data, can have several input RNA-seq data.</description>\n- <version_command>tophat --version</version_command>\n- <requirements>\n- <requirement type="package">tophat</requirement>\n- </requirements>\n- <command interpreter="python">\n-\t tophat_parallel.py\n- ## Change this to accommodate the number of threads you have available.\n- --num-threads="4"\n-\n- ## Provide outputs.\n- -o $outputFileName\n- ##--junctions-output=$junctions\n- ##--hits-output=$accepted_hits\n-\n- ## Handle reference file.\n- #if $refGenomeSource.genomeSource == "history":\n- --own-file=$refGenomeSource.ownFile\n- #else:\n- --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ \'tophat_indexes\' ].get_fields() )[0][-1] }"\n- #end if\n-\n- ## Are reads single-end or paired?\n- --single-paired=$singlePaired.sPaired\n-\n- ## First input file always required.\n- --input1=$input1\n-\n- ## Set params based on whether reads are single-end or paired.\n- #if $singlePaired.sPaired == "single":\n- --settings=$singlePaired.sParams.sSettingsType\n- #if $singlePaired.sParams.sSettingsType == "full":\n- -a $singlePaired.sParams.anchor_length\n- -m $singlePaired.sParams.splice_mismatches\n- -i $singlePaired.sParams.min_intron_length\n- -I $singlePaired.sParams.max_intron_length\n- -F $singlePaired.sParams.junction_filter\n- -g $singlePaired.sParams.max_multihits\n- --min-segment-intron $singlePaired.sParams.min_segment_intron\n- --max-segment-intron $singlePaired.sParams.max_segment_intron\n- --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches\n- --seg-mismatches=$singlePaired.sParams.seg_mismatches\n- --seg-length=$singlePaired.sParams.seg_length\n- --library-type=$singlePaired.sParams.library_type\n- \n- ## Indel search.\n- #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":\n- ## --allow-indels\n- --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length\n- --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length\n- #else:\n- --no-novel-indels\n- #end if\n-\n- ## Supplying junctions parameters.\n- #if $singlePaired.sParams.own_junctions.use_junctions == "Yes":\n- #if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes":\n- -G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model\n- #end if\n- #if $singlePaired.sParams.own_junctions.raw_juncs.use_juncs == "Yes":\n- -j $singlePaired.sParams.own_junctions.raw_juncs.raw_juncs\n- #end if\n- ## TODO: No idea why a string cast is necessary, but it is:\n- #if str($singlePaired.sParams.own_junctions.no_novel_juncs) == "Yes":\n- --no-novel-juncs\n- #end if\n- #end if\n-\n- #if $singlePaired.sParams.closure_search.use_search == "Yes":\n- --closure-search\n- --min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon\n- --'..b'hen such a pair is supported by a split segment alignment of a long read. The default is 500000.\n- -F/--min-isoform-fraction 0.0-1.0 TopHat filters out junctions supported by too few alignments. Suppose a junction spanning two exons, is supported by S reads. Let the average depth of coverage of \n- exon A be D, and assume that it is higher than B. If S / D is less than the minimum isoform fraction, the junction is not reported. A value of zero disables the \n- filter. The default is 0.15.\n- -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many \n- alignments. The default is 40.\n- -G/--GTF [GTF 2.2 file] Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping.\n- -j/--raw-juncs [juncs file] Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive.\n- -no-novel-juncs Only look for junctions indicated in the supplied GFF file. (ignored without -G)\n- --no-closure-search Disables the mate pair closure-based search for junctions. Currently, has no effect - closure search is off by default.\n- --closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (about or less than 50bp)\n- --no-coverage-search Disables the coverage based search for junctions.\n- --coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.\n- --microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.\n- --butterfly-search TopHat will use a slower but potentially more sensitive algorithm to find junctions in addition to its standard search. Consider using this if you expect that your experiment produced a lot of reads from pre-mRNA, that fall within the introns of your transcripts.\n- --segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2.\n- --segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25.\n- --min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50.\n- --min-closure-intron The minimum intron length that may be found during closure search. The default is 50.\n- --max-closure-intron The maximum intron length that may be found during closure search. The default is 5000.\n- --min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50.\n- --max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000.\n- --min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50.\n- --max-segment-intron The maximum intron length that may be found during split-segment search. The default is 500000.\n- </help>\n-</tool>\n' |
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| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/tophat_parallel_unSQL.py --- a/SMART/DiffExpAnal/tophat_parallel_unSQL.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,353 +0,0 @@\n-\n-#!/usr/bin/env python\n-\n-import optparse, os, shutil, subprocess, sys, tempfile, fileinput, tarfile, glob\n-from commons.core.launcher.Launcher import Launcher\n-from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory\n-from commons.core.utils.FileUtils import FileUtils\n-\n-def stop_err( msg ):\n- sys.stderr.write( "%s\\n" % msg )\n- sys.exit()\n-\n-def toTar(tarFileName, accepted_hits_outputNames):\n- tfile = tarfile.open(tarFileName + ".tmp.tar", "w")\n- currentPath = os.getcwd()\n- os.chdir(dir)\n- for file in accepted_hits_outputNames:\n- relativeFileName = os.path.basename(file)\n- tfile.add(relativeFileName)\n- os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))\n- tfile.close()\n- os.chdir(currentPath)\n- \n-def splitFastQ(fileName, nbOfSeqPerBatch):\n- nbOfLinesPerFile = nbOfSeqPerBatch * 4\n- lOutput = []\n- filePrefix, fileExt = os.path.splitext(os.path.basename(fileName))\n- resDir = os.path.dirname(fileName)\n- with open(fileName) as inF:\n- fileNb = 1\n- line = inF.readline()\n- if not line or nbOfLinesPerFile == 0:\n- outFileName = "%s/%s-%s%s" %(resDir, filePrefix, fileNb, fileExt)\n- lOutput.append(outFileName)\n- f = open(outFileName, "wb")\n- shutil.copyfileobj(open(fileName, "rb"), f)\n- f.close()\n- else:\n- while line:\n- outFileName = "%s/%s-%s%s" %(resDir, filePrefix, fileNb, fileExt)\n- lOutput.append(outFileName)\n- with open(outFileName, "w") as outF:\n- lineNb = 1\n- while lineNb <= nbOfLinesPerFile and line:\n- outF.write(line)\n- line = inF.readline()\n- lineNb += 1\n- fileNb += 1\n- return lOutput\n-\n-def joinBAM(dCutOut2Out):\n- for key in dCutOut2Out.keys():\n- fh = open(key, "w") \n- fh.close()\n- nbFile = 0\n- cmd = "samtools merge -f %s" % key\n- for fileName in dCutOut2Out[key]:\n- nbFile = nbFile + 1\n- if nbFile < 225:\n- cmd += " %s" % fileName\n- else:\n- nbFile = 0\n- cmd += ";mv %s tmpBAM;" % (key)\n- cmd += "samtools merge -f %s tmpBAM %s" % (key, fileName)\n- proc = subprocess.Popen( args=cmd , shell=True)\n- returncode = proc.wait()\n-\n- \n-def _map(iLauncher, cmd, cmdStart, cmdFinish ):\n- lCmds = []\n- lCmds.extend(cmd)\n- lCmdStart = []\n- lCmdStart.extend(cmdStart)\n- lCmdFinish = []\n- lCmdFinish.extend(cmdFinish)\n- return(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))\n-\n-def _createTopHatCommand(iLauncher, options, index_paths, inputFileNames, inputRevFilesNames, space):\n- lArgs = []\n- lArgs.append(\'-p %s %s\' % ( options.num_threads, space ))\n- if options.single_paired == \'paired\':\n- lArgs.append(\'-r %s \' % options.mate_inner_dist)\n- if options.settings == \'preSet\':\n- lArgs.append(index_paths)\n- lArgs.append(inputFileNames)\n- if options.input2:\n- lArgs.append(inputRevFilesNames)\n- return iLauncher.getSystemCommand("tophat", lArgs)\n- else:\n- if int( options.min_anchor_length ) >= 3:\n- lArgs.append(\'-a %s \' % options.min_anchor_length)\n- else:\n- raise Exception, \'Minimum anchor length must be 3 or greater\'\n- lArgs.append(\'-m %s \' % options.splice_mismatches)\n- lArgs.append(\'-i %s \' % options.min_intron_length)\n- lArgs.append(\'-I %s \' % options.max_intron_length)\n- if float( options.junction_filter ) != 0.0:\n- lArgs.append(\'-F %s \' % options.junction_filter)\n- lArgs.append(\'-g %s \' % options.max_multihits)\n- # Custom junctions options.\n- if options.gene_model_annotations:\n- lArgs.append(\'-G %s \' % options.gene_'..b'ame + \'\\n\')\n- file.close()\n- out.close()\n- \n- if options.input2:\n- revFile = open(options.input2,"r")\n- lines = revFile.readlines()\n- inputRevFileNames = []\n- for line in lines:\n- revTab = line.split()\n- inputRevFileNames.append(revTab[1])\n- revFile.close()\n-\n- \n- # Creat bowtie index if necessary.\n- tmp_index_dirs = []\n- index_paths = []\n- tmp_index_dir = tempfile.mkdtemp(dir="%s" % os.getcwd())\n- tmp_index_dirs.append(tmp_index_dir)\n- if options.own_file:\n- index_path = os.path.join( tmp_index_dir, \'.\'.join( os.path.split( options.own_file )[1].split( \'.\' )[:-1] ) )\n- index_paths.append(index_path)\n- try:\n- os.link( options.own_file, index_path + \'.fa\' )\n- except:\n- # Tophat prefers (but doesn\'t require) fasta file to be in same directory, with .fa extension\n- pass\n- lCmdsTuples =[]\n- acronym = "tophat_index"\n- jobdb = TableJobAdaptatorFactory.createJobInstance()\n- iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True)\n- cmd_index = iLauncher.getSystemCommand("bowtie-build", [space, "-f %s" % options.own_file, index_path])\n- cmd2Launch = []\n- cmdStart = []\n- cmdFinish = []\n- cmd2Launch.append(cmd_index)\n- lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish)) \n- iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True)\n- else:\n- for file in inputFileNames:\n- tmp_index_dir = tempfile.mkdtemp()\n- index_path = tmp_index_dir + \'/\' + os.path.basename(file).split(\'.\')[0]\n- index_paths.append(index_path)\n- tmp_index_dirs.append(tmp_index_dir)\n-\n- \n- \n- acronym = "tophat"\n- jobdb = TableJobAdaptatorFactory.createJobInstance()\n- iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True)\n- lCmdsTuples = []\n- dCutOut2Out = {}\n- lAllFile2remove = []\n- # for inputFileName in inputFileNames:\n- for i in range(len(inputFileNames)):\n- lCutOutput = []\n- lCutInputFile = splitFastQ(inputFileNames[i], 20000)\n- lAllFile2remove.extend(lCutInputFile)\n- if options.input2:\n- lCutPairInputFile = splitFastQ(inputRevFileNames[i], 20000)\n- lAllFile2remove.extend(lCutPairInputFile)\n- for j in range(len(lCutInputFile)):\n- cutOutput = "%s_out" % lCutInputFile[j]\n- lCutOutput.append(cutOutput)\n- lAllFile2remove.extend(lCutOutput)\n- cmd2Launch = []\n- if options.input2: \n- inputRevFile = lCutPairInputFile[j]\n- else:\n- inputRevFile = ""\n- if options.own_file:\n- cmd2Launch.append(_createTopHatCommand(iLauncher, options, index_paths[0], lCutInputFile[j], inputRevFile, space))\n- else:\n- cmd2Launch.append(_createTopHatCommand(iLauncher, options, index_paths[i], lCutInputFile[j], inputRevFile, space))\n- cmdStart = []\n- cmdFinish = ["shutil.copyfile( os.path.join( \'tophat_out\', \'accepted_hits.bam\' ), \'%s\')" % cutOutput]\n- lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish)) \n- dCutOut2Out[accepted_hits_outputNames[i]] = lCutOutput\n- iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True)\n- \n- joinBAM(dCutOut2Out) \n- FileUtils.removeFilesFromListIfExist(lAllFile2remove) \n- \n- if options.outputTar != None:\n- toTar(options.outputTar, accepted_hits_outputNames)\n-\n- \n- # Clean up temp dirs\n- for tmp_index_dir in tmp_index_dirs:\n- if os.path.exists( tmp_index_dir ):\n- shutil.rmtree( tmp_index_dir )\n-\n- for tmp in tmp_files:\n- os.remove(tmp)\n-\n-\n-if __name__=="__main__": __main__()\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/tophat_parallel_unSQL.xml --- a/SMART/DiffExpAnal/tophat_parallel_unSQL.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,577 +0,0 @@\n-<tool id="tophat_parallel_unSQL" name="Tophat for Illumina (for DEA in parallel)" version="1.0.0">\n- <description>Find splice junctions using RNA-seq data, can have several input RNA-seq data (parallelized).</description>\n- <version_command>tophat --version</version_command>\n- <requirements>\n- <requirement type="package">tophat</requirement>\n- </requirements>\n- <command interpreter="python">\n-\t tophat_parallel_unSQL.py\n- ## Change this to accommodate the number of threads you have available.\n- --num-threads="4"\n-\n- ## Provide outputs.\n- -o $outputFileName\n- ##--junctions-output=$junctions\n- ##--hits-output=$accepted_hits\n-\n- ## Handle reference file.\n- #if $refGenomeSource.genomeSource == "history":\n- --own-file=$refGenomeSource.ownFile\n- #else:\n- --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ \'tophat_indexes\' ].get_fields() )[0][-1] }"\n- #end if\n-\n- ## Are reads single-end or paired?\n- --single-paired=$singlePaired.sPaired\n-\n- ## First input file always required.\n- --input1=$input1\n-\n- ## Set params based on whether reads are single-end or paired.\n- #if $singlePaired.sPaired == "single":\n- --settings=$singlePaired.sParams.sSettingsType\n- #if $singlePaired.sParams.sSettingsType == "full":\n- -a $singlePaired.sParams.anchor_length\n- -m $singlePaired.sParams.splice_mismatches\n- -i $singlePaired.sParams.min_intron_length\n- -I $singlePaired.sParams.max_intron_length\n- -F $singlePaired.sParams.junction_filter\n- -g $singlePaired.sParams.max_multihits\n- --min-segment-intron $singlePaired.sParams.min_segment_intron\n- --max-segment-intron $singlePaired.sParams.max_segment_intron\n- --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches\n- --seg-mismatches=$singlePaired.sParams.seg_mismatches\n- --seg-length=$singlePaired.sParams.seg_length\n- --library-type=$singlePaired.sParams.library_type\n- \n- ## Indel search.\n- #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":\n- ## --allow-indels\n- --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length\n- --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length\n- #else:\n- --no-novel-indels\n- #end if\n-\n- ## Supplying junctions parameters.\n- #if $singlePaired.sParams.own_junctions.use_junctions == "Yes":\n- #if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes":\n- -G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model\n- #end if\n- #if $singlePaired.sParams.own_junctions.raw_juncs.use_juncs == "Yes":\n- -j $singlePaired.sParams.own_junctions.raw_juncs.raw_juncs\n- #end if\n- ## TODO: No idea why a string cast is necessary, but it is:\n- #if str($singlePaired.sParams.own_junctions.no_novel_juncs) == "Yes":\n- --no-novel-juncs\n- #end if\n- #end if\n-\n- #if $singlePaired.sParams.closure_search.use_search == "Yes":\n- --closure-search\n- --min-closure-exon $singlePaired.sParams.closure_search.min_c'..b'hen such a pair is supported by a split segment alignment of a long read. The default is 500000.\n- -F/--min-isoform-fraction 0.0-1.0 TopHat filters out junctions supported by too few alignments. Suppose a junction spanning two exons, is supported by S reads. Let the average depth of coverage of \n- exon A be D, and assume that it is higher than B. If S / D is less than the minimum isoform fraction, the junction is not reported. A value of zero disables the \n- filter. The default is 0.15.\n- -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many \n- alignments. The default is 40.\n- -G/--GTF [GTF 2.2 file] Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping.\n- -j/--raw-juncs [juncs file] Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive.\n- -no-novel-juncs Only look for junctions indicated in the supplied GFF file. (ignored without -G)\n- --no-closure-search Disables the mate pair closure-based search for junctions. Currently, has no effect - closure search is off by default.\n- --closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (about or less than 50bp)\n- --no-coverage-search Disables the coverage based search for junctions.\n- --coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.\n- --microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.\n- --butterfly-search TopHat will use a slower but potentially more sensitive algorithm to find junctions in addition to its standard search. Consider using this if you expect that your experiment produced a lot of reads from pre-mRNA, that fall within the introns of your transcripts.\n- --segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2.\n- --segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25.\n- --min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50.\n- --min-closure-intron The minimum intron length that may be found during closure search. The default is 50.\n- --max-closure-intron The maximum intron length that may be found during closure search. The default is 5000.\n- --min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50.\n- --max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000.\n- --min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50.\n- --max-segment-intron The maximum intron length that may be found during split-segment search. The default is 500000.\n- </help>\n-</tool>\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/DiffExpAnal/wrappGSNAP.py --- a/SMART/DiffExpAnal/wrappGSNAP.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,76 +0,0 @@ -#! /usr/bin/env python - -import os, sys, subprocess,tempfile -from optparse import OptionParser - -def stop_err(msg): - sys.stderr.write('%s\n' % msg) - sys.exit() - -def __main__(): - #Parse Command Line - description = "GMAP/GSNAP version:2012-12-20." - parser = OptionParser(description = description) - parser.add_option("-d", "--genomeName", dest="genomeName", help="Define the reference genome name.[compulsory]") - parser.add_option("-o", "--outputFile", dest="outputfile", help="output[compulsory]") - #parser.add_option("-D", "--workingDir", dest="workingdir", help="Define the directory of writing reference genome index.[compulsory]") - parser.add_option("-k", "--kmer", dest="kmer", default=12, help="Choose kmer value (<=16), a big kmer value can take more RAM(4Go).[compulsory]") - parser.add_option("-i", "--inputFasta", dest="inputFastaFile", help="Reference genome file, fasta format.[compulsory]") - parser.add_option("-q", "--inputFastq", dest="inputFastqFile", help="Input fastq file.") - parser.add_option("-p", "--pairedEnd", dest="pairedEndFile", default=None, help="Input paired-end fastq file.") - parser.add_option("-A", "--outputFormat", dest="outputFormat", default="sam", help="Choose an output format [sam, goby (need to re-compile with appropriate options)].") - (options, args) = parser.parse_args() - - #If workingDir dose not exist, should create before run the job. - - workingDir = os.path.dirname(options.inputFastaFile) - - cmds = [] - cmd_setup = "gmap_setup -d %s -D %s -k %s %s" % (options.genomeName, workingDir, options.kmer, options.inputFastaFile) - cmds.append(cmd_setup) - cmd_make_coords = "make -f Makefile.%s coords" % options.genomeName - cmds.append(cmd_make_coords) - cmd_make_gmapdb = "make -f Makefile.%s gmapdb" % options.genomeName - cmds.append(cmd_make_gmapdb) - cmd_make_install = "make -f Makefile.%s install" % options.genomeName - cmds.append(cmd_make_install) - cmd_run = "gsnap -d %s -D %s -A %s %s " % (options.genomeName, workingDir, options.outputFormat, options.inputFastqFile) - if options.pairedEndFile != None: - cmd_run += "%s" % options.pairedEndFile - cmd_run += " > %s" % options.outputfile - cmds.append(cmd_run) - - tmp_files = [] - for i in range(len(cmds)): - try: - tmp_out = tempfile.NamedTemporaryFile().name - tmp_files.append(tmp_out) - tmp_stdout = open(tmp_out, 'wb') - tmp_err = tempfile.NamedTemporaryFile().name - tmp_files.append(tmp_err) - tmp_stderr = open(tmp_err, 'wb') - proc = subprocess.Popen(args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr) - returncode = proc.wait() - tmp_stderr.close() - #get stderr, allowing for case where it's very large - tmp_stderr = open(tmp_err, 'rb') - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read(buffsize) - if not stderr or len(stderr) % buffsize != 0: - break - except OverflowError: - pass - tmp_stdout.close() - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - except Exception, e: - stop_err('Error in :\n' + str(e)) - - for tmp_file in tmp_files: - os.remove(tmp_file) - -if __name__=="__main__":__main__() |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/changeName.py --- a/SMART/bacteriaRegulatoryRegion_Detection/changeName.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,99 +0,0 @@ -#! /usr/bin/env python - -import optparse, os, sys, subprocess, tempfile, shutil -from optparse import OptionParser - -def stop_err(msg): - sys.stderr.write('%s\n' % msg) - sys.exit() - -def changeName(fileName, format, name, outputName): - file = open(fileName, 'r') - line = file.readline() - if format == "fasta": - while not line.startswith('>'): - line = file.readline() - old_name = line[1:] - elif format == "gff": - while line.startswith('#'): - line = file.readline() - old_name = (line.split('\t'))[0] - elif format == "sam": - while line.startswith('@'): - line = file.readline() - old_name = (line.split('\t'))[2] - file.close() - cmd = "sed \"s/%s/%s/g\" %s >%s " % (old_name.strip(), name.strip(), fileName, outputName) - proc = subprocess.Popen(cmd, shell=True) - proc.communicate() - if proc.returncode != 0: - raise Exception("ERROR when launching '%s'" % cmd) - -def getName(fileName, format): - file = open(fileName, 'r') - line = file.readline() - if format == "gff": - while line.startswith('#'): - line = file.readline() - old_name = (line.split('\t'))[0] - elif format == "sam": - while line.startswith('@') or line.startswith('#'): - line = file.readline() - old_name = (line.split('\t'))[2] - file.close() - return old_name - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option("", "--input1", dest="inputFile1", default=None, help="Choose a fasta file.") - parser.add_option("", "--input2", dest="inputFile2", default=None, help="Choose a gff file.") - parser.add_option("", "--input3", dest="inputFile3", default=None, help="Choose a sam file.") - parser.add_option("", "--name", dest="name", default=None, help="Change to a new name.[compulsory] if there is only one input.") - parser.add_option("", "--output1", dest="outputFile1", default=None, help="OutputFile1") - parser.add_option("", "--output2", dest="outputFile2", default=None, help="OutputFile2") - parser.add_option("", "--output3", dest="outputFile3", default=None, help="OutputFile3") - (options, args) = parser.parse_args() - -#TODO:write raise Exception!! - - #In case only one input - if options.name == None: - #find a default_name to unify the name for all input files - if options.inputFile1 != None: - if options.inputFile2 == None and options.inputFile3 == None: - raise Exception("ERROR, only one input, you should identify a new name to modify.") - elif options.inputFile2 != None and options.outputFile2 != None: - default_name = getName(options.inputFile2, 'gff') - changeName(options.inputFile1, 'fasta', default_name, options.outputFile1) - changeName(options.inputFile2, 'gff', default_name, options.outputFile2) - if options.inputFile3 != None and options.outputFile3 != None: - changeName(options.inputFile3, 'sam', default_name, options.outputFile3) - elif options.inputFile3 != None and options.outputFile3 != None: - default_name = getName(options.inputFile3, 'sam') - changeName(options.inputFile3, 'sam', default_name, options.outputFile3) - changeName(options.inputFile1, 'fasta', default_name, options.outputFile1) - if options.inputFile2 != None and options.outputFile2 != None: - changeName(options.inputFile2, 'gff', default_name, options.outputFile2) - else: - if options.inputFile1 != None and options.outputFile1 != None: - changeName(options.inputFile1, 'fasta', options.name, options.outputFile1) - if options.inputFile2 != None and options.outputFile2 != None: - changeName(options.inputFile2, 'gff', options.name, options.outputFile2) - if options.inputFile3 != None and options.outputFile3 != None: - changeName(options.inputFile3, 'sam', options.name, options.outputFile3) - -if __name__ == '__main__':__main__() - - -#test commands: -#only one input: -#python changeName.py --input1 NC_011744.fna --name NC_test --output1 out.fna -#several inputs: -#python changeName.py --input1 NC_011744.fna --input2 NC_011744.gff --output1 out.fna --output2 out.gff -#python changeName.py --input1 NC_011744.fna --input2 NC_011744.gff --name NC_test --output1 out.fna --output2 out.gff -#python changeName.py --input1 NC_011744.fna --input2 NC_011744.gff --input3 NC_011744.sam --name NC_test2 --output1 out.fna --output2 out.gff --output3 out.sam -#python changeName.py --input1 NC_011744.fna --input3 out.sam --output1 out.fna --output3 out.sam - - - \ No newline at end of file |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/changeName.xml --- a/SMART/bacteriaRegulatoryRegion_Detection/changeName.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,80 +0,0 @@ -<tool id="changeName" name="changeName"> - <description>Change the chromosome name or gene name of a singla fasta, gff or sam file. For this tool, it can not treat mutiple-chromosome, gene files.</description> - <command interpreter="python"> - changeName.py - #if $optionFasta.fastaFile == 'Yes': - --input1 $optionFasta.fasta --output1 $outputFasta - #end if - #if $optionGff.gffFile == 'Yes': - --input2 $optionGff.gff --output2 $outputGff - #end if - #if $optionSam.samFile == 'Yes': - --input3 $optionSam.sam --output3 $outputSam - #end if - #if $optionName.name == 'Yes': - --name $optionName.nameValue - #end if - </command> - - <inputs> - <conditional name="optionFasta"> - <param name="fastaFile" type="select" label="You can choose a fasta input file to change the name." > - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="fasta" format="fasta" type="data" label="Identify you fasta input file."/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="optionGff"> - <param name="gffFile" type="select" label="You can choose a supplementary gff input file to change the name." > - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="gff" format="gff" type="data" label="Identify you gff input file."/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="optionSam"> - <param name="samFile" type="select" label="You can choose a supplementary sam input file to change the name." > - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="sam" format="sam" type="data" label="Identify you sam input file."/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="optionName"> - <param name="name" type="select" label="Identify a new name to change." > - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="nameValue" type="text" value="None" label="Identify the new name."/> - </when> - <when value="No"> - </when> - </conditional> - </inputs> - - <outputs> - <data name="outputFasta" format="fasta"> - <filter>optionFasta['fastaFile'] == 'Yes'</filter> - </data> - <data format="gff" name="outputGff" > - <filter>optionGff['gffFile'] == 'Yes'</filter> - </data> - <data format="sam" name="outputSam" > - <filter>optionSam['samFile'] == 'Yes'</filter> - </data> - </outputs> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/colorGff.pl --- a/SMART/bacteriaRegulatoryRegion_Detection/colorGff.pl Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,71 +0,0 @@ -#!/usr/bin/perl -w -### -# But : ajout ou modif de couleur d'un gff -# -# Entrees : fichier gff -# -# Sortie : gff affiche a l'ecran -# -###------------------------------------------------------ -use vars qw($USAGE); -use strict; - -=head1 NAME - -colorGff.pl - add or change color of a gff file - -=head1 SYNOPSIS - -% colorGff.pl -i file.gff -c color [-h] - -=head1 DESCRIPTION -This script will parse DOOR repport file and write information in gff3 format. - - -i|--input fileName gff input file name - -c|--color RGBcode RGB code for color - -o|--output fileName gff3 output file name - [-h|--help] help mode then die - -=head1 AUTHOR - Claire Toffano-Nioche - jan.11 - -=cut -#----------------------- -my ($fileName, $colourGff, $outFileName) = ("", "", "colorOut.gff3") ; - # command line check - foreach my $num (0 .. $#ARGV) { - SWITCH: for ($ARGV[$num]) { - /--input|-i/ && do { - $fileName=$ARGV[$num+1]; - open ( fichierGff, "< $fileName" ) or die "Can't open gff file: \"$fileName\"\n" ; - last }; - /--color|-c/ && do { - $colourGff =$ARGV[$num+1]." ".$ARGV[$num+2]." ".$ARGV[$num+3]; - last }; -# /--output|-o/ && do { -# $outFileName=$ARGV[$num+1]; -# last }; - /--help|-h/ && do { exec("pod2text $0\n") ; die }; - } - } -# open(OUT,">$outFileName") or die "Error can't $outFileName open for output. $!\n"; - # informations retrieval - my @lines = <fichierGff> ; - close fichierGff ; - # treatment - #print "gff file read ; number of lines : $#lines\n"; - for (my $i=0 ; $i <= $#lines ; $i++) { - if ($lines[$i] =~ /;/) { - if ($lines[$i] =~ /color=/) { - $lines[$i] =~ s/color=.*;/color=$colourGff;/ ; - } else { # add colour - $lines[$i] =~ s/;/;color=$colourGff;/ ; - } - } else { # (no = gff bug if col9 begin with semi-coma ?) or only one tag : add color tag - chomp($lines[$i]) ; - $lines[$i] .= "; color=".$colourGff.";\n"; - } -# print OUT $lines[$i] ; - print $lines[$i]; - } -# close OUT ; -exit(0); |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/colorGff.xml --- a/SMART/bacteriaRegulatoryRegion_Detection/colorGff.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,19 +0,0 @@ -<tool id="colorGff" name="colorGff"> - <description> Parses a DOOR report file and writes the information in a gff3 out file. </description> - <command interpreter="perl"> - colorGff.pl -i $inputFile -c $RGBcode > $outputFile - </command> - - <inputs> - <param name="inputFile" type="data" label="Input File" format="gff"/> - <param name="RGBcode" type="text" value="250 128 114" help="RGB code is necessary for choosing the color."/> - </inputs> - - <outputs> - <data format="gff3" name="outputFile" label="[colorGff] Output File"/> - </outputs> - - <help> - Command example: perl colorGff.pl -i trans_covUp5_nbEUp10_lgUp50.gff3 -c "250 128 114" > trans_covUp5_nbEUp10_lgUp50_c.gff3 - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/coverageGff.pl --- a/SMART/bacteriaRegulatoryRegion_Detection/coverageGff.pl Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,74 +0,0 @@ -#!/usr/bin/perl -w -### -# But : ajout ou modif de la couverture d'un gff -# -# Entrees : fichier gff -# -# Sortie : gff affiche a l'ecran -# -###------------------------------------------------------ - -#!/usr/bin/perl -w - -use vars qw($USAGE); -use strict; - -=head1 NAME - -coverageGff.pl - add or compute the coverage of a gff file - -=head1 SYNOPSIS - -% coverageGff.pl -i file.gff -l readLength [-h] - -=head1 DESCRIPTION -This script will parse gff file, compute read coverage form the "nbElements" tag and write coverage in gff3 format. - - -i|--input fileName gff input file name - -l|--length ReadLength lenght of the reads in bp [38 default] - -o|--output fileName gff3 output file name - [-h|--help] help mode then die - -=head1 AUTHOR - Claire Toffano-Nioche - fev.11 - -=cut -#----------------------- -my ($fileName, $length, $outFileName) = ("", 38, "coverageOut.gff3") ; - # command line check - foreach my $num (0 .. $#ARGV) { - SWITCH: for ($ARGV[$num]) { - /--input|-i/ && do { - $fileName=$ARGV[$num+1]; - open ( fichierGff, "< $fileName" ) or die "Can't open gff file: \"$fileName\"\n" ; - last }; - /--length|-l/ && do { - $length=$ARGV[$num+1]; - last }; - /--help|-h/ && do { exec("pod2text $0\n") ; die }; - } - } - # informations retrieval -# open(OUT,">$outFileName") or die "Error can't $outFileName open for output. $!\n"; - my @lines = <fichierGff> ; - close fichierGff ; - # treatment - #print "gff file read ; number of lines : $#lines\n"; - for (my $i=0 ; $i <= $#lines ; $i++) { - # compute coverage : - if ($lines[$i] =~ /nbElements=/) { - my ($nbE)=($lines[$i] =~ /nbElements=(\d+)/) ; - my @gffCol=split("\t", $lines[$i]) ; - # print "ligne : $i, nbE : $nbE, length : $length, debut : $gffCol[3], fin : $gffCol[4].\n"; - my $cover=$length*$nbE/($gffCol[4]-$gffCol[3]+1) ; - $cover=int(100*$cover+0.5)/100 ; # arronri sup. precision 2 chiffres - if ($lines[$i] =~ /coverage=/) { # replace coverage - $lines[$i] =~ s/coverage=.*;/coverage=$cover;/ ; - } else { # add coverage - $lines[$i] =~ s/;/;coverage=$cover;/ ; - } - } -# print OUT $lines[$i] ; - print $lines[$i] ; - } -#close OUT ; -exit(0); |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/coverageGff.xml --- a/SMART/bacteriaRegulatoryRegion_Detection/coverageGff.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,17 +0,0 @@ -<tool id="coverageGff" name="coverage Gff"> - <description>Computes reads coverage form a "nbElements" tag and writes the calculated coverage in a gff3 out file.</description> - <command interpreter="perl"> coverageGff.pl -i $inputFile -l $readSize > $outputFile </command> - <inputs> - <param name="inputFile" type="data" label="Input File" format="gff"/> - <param name="readSize" type="integer" value="38" help="The size of read, default: 38nt"/> - - </inputs> - - <outputs> - <data format="gff3" name="outputFile" label="[coveragePl] Output File"/> - </outputs> - - <help> - command example: perl coverageGff.pl -i *_trans_inIG.gff > *_trans_inIG_cov.gff - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/interElementGff.pl --- a/SMART/bacteriaRegulatoryRegion_Detection/interElementGff.pl Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,187 +0,0 @@ -#!/usr/bin/perl -w -### -# But : protocol permettant la detection d'RNA non codant potentiel -# -# Entrees : fichier de mapping Smart gff3 -# fichier gff des gènes -# fichier gff des clusters Cis regulateur potentiel -# -# Sortie : fichier gff des clusters ARN nc -# -###------------------------------------------------------ -use vars qw($USAGE); -use strict; - -=head1 NAME - -interElementGff.pl - creation of a new Gff corresponding to the region of two successive Elements - -=head1 SYNOPSIS - -% interElementGff.pl -i inputFile.gff3 -o outputFile.gff3 [-s 50] [-a 20] [-n seqName] [-h] - -=head1 DESCRIPTION -This script will determine cluster ok ncRNA. - - -i|--input fileName gff input file name - -o|--output fileName gff output file name - -n|--name seqName sequence name - -p|--print print parameters used - - -f5ff n number of nt to exclude from 5' seed when gene before is Forward, seed is Forward and next gene is Forward [default 0] - -ff3f n number... " ...[default 0] - - -f5fr n number... " ...[default 0] - -ff3r n number... " ...[default 0] - - -fr3f n number... " ...[default 0] - -fr5f n number... " ...[default 0] - - -f3rr n number... " ...[default 0] - -fr5r n number... " ...[default 0] - - -r5ff n number... " ...[default 0] - -rf3f n number... " ...[default 0] - - -r5fr n number... " ...[default 0] - -rf3r n number... " ...[default 0] - - -r3rf n number... " ...[default 0] - -rr5f n number... " ...[default 0] - - -r3rr n number... " ...[default 0] - -rr5r n number... " ...[default 0] - - [-h|--help] help mode then die - - -USAGE_CASE - -% interElementGff.pl -i inputFile.gff3 -o outputFile.gff3 -ff 53 -rr 23 -n NC_011744 - -BUG - -Caution : input file needs to be sorted on positions - -Caution : for -f/r options add +3 bp to include stop codon if not in input file - -=head1 AUTHOR - CTN - apr.11 -(from RNA-Vibrio/protocol_NC_V2.pl - Claire KUCHLY) - -=cut -#---------------------------------------------------------------------------- -# check command line : -my ($IDfile, $OutputFileName, $f5ff, $ff3f, $f5fr, $ff3r, $f3rf, $fr5f, $f3rr,$fr5r, $r5ff, $rf3f, $r5fr, $rf3r, $r3rf, $rr5f, $r3rr, $rr5r, $seqName, $printParameters) = - (undef, undef , 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, "", 0) ; -if ($#ARGV==0) { - die (exec("pod2text $0\n")); -} else { - foreach my $num (0 .. $#ARGV) { - SWITCH: for ($ARGV[$num]) { - /--input|-i/ && do { $IDfile=$ARGV[$num+1]; - open(F,"<$IDfile") or die "Error: Can't open \"$IDfile\", $!"; - last; }; - /-f5ff/ && do { $f5ff=$ARGV[$num+1]+1; last; }; # need +1 for intervall computations - /-ff3f/ && do { $ff3f=$ARGV[$num+1]+1; last; }; - - /-f5fr/ && do { $f5fr=$ARGV[$num+1]+1; last; }; - /-ff3r/ && do { $ff3r=$ARGV[$num+1]+1; last; }; - - /-f3rf/ && do { $f3rf=$ARGV[$num+1]+1; last; }; - /-fr5f/ && do { $fr5f=$ARGV[$num+1]+1; last; }; - - /-f3rr/ && do { $f3rr=$ARGV[$num+1]+1; last; }; - /-fr5r/ && do { $fr5r=$ARGV[$num+1]+1; last; }; - - /-r5ff/ && do { $r5ff=$ARGV[$num+1]+1; last; }; - /-rf3f/ && do { $rf3f=$ARGV[$num+1]+1; last; }; - - /-r5fr/ && do { $r5fr=$ARGV[$num+1]+1; last; }; - /-rf3r/ && do { $rf3r=$ARGV[$num+1]+1; last; }; - - /-r3rf/ && do { $r3rf=$ARGV[$num+1]+1; last; }; - /-rr5f/ && do { $rr5f=$ARGV[$num+1]+1; last; }; - - /-r3rr/ && do { $r3rr=$ARGV[$num+1]+1; last; }; - /-rr5r/ && do { $rr5r=$ARGV[$num+1]+1; last; }; - -# /--name|-n/ && do { $seqName=$ARGV[$num+1]; last; }; - /--print|-p/ && do { $printParameters=1; last; }; - /--output|-o/ && do { $OutputFileName=$ARGV[$num+1]; - open(S,">$OutputFileName") or die "Error : Can't open result file \"$OutputFileName\", $!"; - last; }; - /--help|-h/ && do { exec("pod2text $0\n") ; die }; - } - } - if ($printParameters) { - print " - --> f5ff ",$f5ff-1," --> ff3f ",$ff3f-1," --> ; - --> f5fr ",$f5fr-1," --> ff3r ",$ff3r-1," <-- ; - --> f3rf ",$f3rf-1," <-- fr5f ",$fr5f-1," --> ; - --> f3rr ",$f3rr-1," <-- fr5r ",$fr5r-1," <-- ; - <-- r5ff ",$r5ff-1," --> rf3f ",$rf3f-1," --> ; - <-- r5fr ",$r5fr-1," --> rf3r ",$rf3r-1," <-- ; - <-- r3rf ",$r3rf-1," <-- rr5f ",$rr5f-1," --> ; - <-- r3rr ",$r3rr-1," <-- rr5r ",$rr5r-1," <-- ;\n"; - } - ##NC_011753.2 RefSeq gene 367 834 . - . locus_tag=VS_0001;db_xref=GeneID:7162789 - my $finSeedSens; - my $finSeedAntisens; - my $debSeedSens; - my $debSeedAntisens; - my $info_gene=""; - my $sensGeneAvant = "+" ; # 1rst seed definition : geneAvant (gene[i-1]) doesn't exist - my @chromList; - while(my $ligne = <F>){ - chomp($ligne); - my @list = split(/\t/,$ligne); - if ((scalar(@chromList) == 0) or ($chromList[$#chromList] ne $list[0])){ - push(@chromList, $list[0]); - my $finSeedSens; - my $finSeedAntisens; - my $debSeedSens; - my $debSeedAntisens; - my $info_gene=""; - my $sensGeneAvant = "+" ; # 1rst seed definition : geneAvant (gene[i-1]) doesn't exist - } - if (($sensGeneAvant eq "+") and ($list[6] eq "+")) { #CTN ie geneavant == f, geneapres == f - $debSeedSens += $f5ff; - $finSeedSens = $list[3]- $ff3f; - $debSeedAntisens += $f3rf; - $finSeedAntisens = $list[3]- $fr5f; - } elsif (($sensGeneAvant eq "+") and ($list[6] eq "-")) { #CTN ie geneaavant == f, geneapres == r - $debSeedSens += $f5fr; - $finSeedSens = $list[3]- $ff3r; - $debSeedAntisens += $f3rr; - $finSeedAntisens = $list[3]- $fr5r; - } elsif (($sensGeneAvant eq "-") and ($list[6] eq "+")) { #CTN ie geneaavant == r, geneapres == f - $debSeedSens += $r5ff; - $finSeedSens = $list[3]- $rf3f; - $debSeedAntisens += $r3rf; - $finSeedAntisens = $list[3]- $rr5f; - } else { #CTN ie geneaavant == r, geneapres == r - $debSeedSens += $r5fr; - $finSeedSens = $list[3]- $rf3r; - $debSeedAntisens += $r3rr; - $finSeedAntisens = $list[3]- $rr5r; - } - if ($debSeedSens <= 0) { $debSeedSens=1 ; } # 1srt - if ($debSeedAntisens <= 0) { $debSeedAntisens=1 ; } - if($debSeedSens < $finSeedSens){ # only "real" seed - #print "$gene_avant\nNC_011753\tperso\tseed\t$deb_seed\t$fin_seed\t.\t+\t.\tgeneavant=$info_gene;geneapres=$list[@list-1]\n$ligne\n\n"; - # - - print S "$list[0]\tperso\tseedIR\t$debSeedSens\t$finSeedSens\t.\t+\t.\tgeneavant=$info_gene;geneapres=$list[@list-1]\n"; - } - if ($debSeedAntisens < $finSeedAntisens){ - print S "$list[0]\tperso\tseedIR\t$debSeedAntisens\t$finSeedAntisens\t.\t-\t.\tgeneavant=$info_gene;geneapres=$list[@list-1]\n"; - } - $sensGeneAvant = $list[6] ; # GFF : column 6 gives strand - $debSeedSens = $list[4]; - $debSeedAntisens = $list[4]; - $info_gene = $list[@list-1]; - } - close F; - close S; - exit(0); -} |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/interElementGff.xml --- a/SMART/bacteriaRegulatoryRegion_Detection/interElementGff.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,284 +0,0 @@ -<tool id="interElementGff" name="interElementGff"> - <description>Creates a new Gff output, which corresponds to the region of two successive Elements. </description> - <command interpreter="perl"> - interElementGff.pl -i $inputFile - - #if $Optionf5ff.option == "Yes": - -f5ff $Optionf5ff.f5ffValue - #end if - - #if $Optionff3f.option == "Yes": - -ff3f $Optionff3f.ff3fValue - #end if - - #if $Optionf5fr.option == "Yes": - -f5fr $Optionf5fr.f5frValue - #end if - - #if $Optionff3r.option == "Yes": - -ff3r $Optionff3r.ff3rValue - #end if - - #if $Optionf3rf.option == "Yes": - -f3rf $Optionf3rf.f3rfValue - #end if - - #if $Optionfr5f.option == "Yes": - -fr5f $Optionfr5f.fr5fValue - #end if - - #if $Optionf3rr.option == "Yes": - -f3rr $Optionf3rr.f3rrValue - #end if - - #if $Optionfr5r.option == "Yes": - -fr5r $Optionfr5r.fr5rValue - #end if - - #if $Optionr5ff.option == "Yes": - -r5ff $Optionr5ff.r5ffValue - #end if - - #if $Optionrf3f.option == "Yes": - -rf3f $Optionrf3f.rf3fValue - #end if - - #if $Optionr5fr.option == "Yes": - -r5fr $Optionr5fr.r5frValue - #end if - - #if $Optionrf3r.option == "Yes": - -rf3r $Optionrf3r.rf3rValue - #end if - - #if $Optionr3rf.option == "Yes": - -r3rf $Optionr3rf.r3rfValue - #end if - - #if $Optionrr5f.option == "Yes": - -rr5f $Optionrr5f.rr5fValue - #end if - - #if $Optionr3rr.option == "Yes": - -r3rr $Optionr3rr.r3rrValue - #end if - - #if $Optionrr5r.option == "Yes": - -rr5r $Optionrr5r.rr5rValue - #end if - - -o $outputFile - </command> - - <inputs> - <param name="inputFile" type="data" label="Input File" format="gff"/> - - <conditional name="Optionf5ff"> - <param name="option" type="select" label="Option[f5ff]" help="number of nt to exclude from 5' seed when gene before is Forward, seed is Forward and next gene is Forward [default 0]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="f5ffValue" type="integer" value="10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionff3f"> - <param name="option" type="select" label="Option[ff3f]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="ff3fValue" type="integer" value="30"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionf5fr"> - <param name="option" type="select" label="Option[f5fr]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="f5frValue" type="integer" value="10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionff3r"> - <param name="option" type="select" label="Option[ff3r]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="ff3rValue" type="integer" value="-10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionf3rf"> - <param name="option" type="select" label="Option[f3rf]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="f3rfValue" type="integer" value="-10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionfr5f"> - <param name="option" type="select" label="Option[fr5f]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="fr5fValue" type="integer" value="10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionf3rr"> - <param name="option" type="select" label="Option[f3rr]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="f3rrValue" type="integer" value="-10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionfr5r"> - <param name="option" type="select" label="Option[fr5r]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="fr5rValue" type="integer" value="10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionr5ff"> - <param name="option" type="select" label="Option[r5ff]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="r5ffValue" type="integer" value="10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionrf3f"> - <param name="option" type="select" label="Option[rf3f]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="rf3fValue" type="integer" value="30"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionr5fr"> - <param name="option" type="select" label="Option[r5fr]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="r5frValue" type="integer" value="10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionrf3r"> - <param name="option" type="select" label="Option[rf3r]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="rf3rValue" type="integer" value="-10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionr3rf"> - <param name="option" type="select" label="Option[r3rf]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="r3rfValue" type="integer" value="30"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionrr5f"> - <param name="option" type="select" label="Option[rr5f]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="rr5fValue" type="integer" value="10"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionr3rr"> - <param name="option" type="select" label="Option[r3rr]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="r3rrValue" type="integer" value="30"/> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="Optionrr5r"> - <param name="option" type="select" label="Option[rr5r]"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="rr5rValue" type="integer" value="10"/> - </when> - <when value="No"> - </when> - </conditional> - - </inputs> - - <outputs> - <data name="outputFile" format="gff" label="[interElementGff] Output File"/> - </outputs> - - <help> - command example: interElementGff.pl -i ${i}_annot.gff -o ${i}_trans_IG.gff -f5ff 10 -ff3f 30 -f5fr 10 -ff3r -10 -f3rf -10 -fr5f 10 -f3rr -10 -fr5r 10 -r5ff 10 -rf3f 30 -r5fr 10 -rf3r -10 -r3rf 30 -rr5f 10 -r3rr 30 -rr5r 10 - </help> - -</tool> - - - - - - |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/listGff.sh --- a/SMART/bacteriaRegulatoryRegion_Detection/listGff.sh Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,3 +0,0 @@ -#!/bin/bash -awk '{print $3}' $1 | grep "[[:alpha:]]" | sort -n | uniq -c - |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/prepareAnnot.sh --- a/SMART/bacteriaRegulatoryRegion_Detection/prepareAnnot.sh Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -#!/bin/bash -python $GALAXY_ROOT/tools/repet_pipe/SMART/Java/Python/clusterize.py -f gff -i $1 -o intermedia.gff3 -c -d 150 -awk '{if ($3!="exon") {print $0}}' intermedia.gff3 > intermedia.gff -#perl sortGff.pl -i intermedia.gff > $2 -python $GALAXY_ROOT/tools/repet_pipe/SMART/Java/Python/CollapseReads.py -i intermedia.gff -f gff -o $2 |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/prepareAnnot.xml --- a/SMART/bacteriaRegulatoryRegion_Detection/prepareAnnot.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,15 +0,0 @@ -<tool id="prepareAnnotation" name="prepare annotation file"> - <description>Prepares Annotation file -> clusterizes, filters exon and sorts annotations.</description> - <command interpreter="bash"> prepareAnnot.sh $inputFile $outputFile </command> - <inputs> - <param name="inputFile" type="data" label="Input File" format="gff"/> - </inputs> - - <outputs> - <data format="gff3" name="outputFile" label="[prepareAnnotation] Output File"/> - </outputs> - - <help> - command example: sh prepareAnnot.sh NC_011744r_annot_tmp1.gff NC_011744r_annot_pre1.gff - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/seedGff.pl --- a/SMART/bacteriaRegulatoryRegion_Detection/seedGff.pl Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,91 +0,0 @@ -#!/usr/bin/perl -w -### -# But : extension des UTR5 à partir des clusters de reads -# -# Entrees : fichier gff annotation + cluster -# -# Sortie : UTR5.gff -# -###------------------------------------------------------ -use vars qw($USAGE); -use strict; -use Getopt::Long; - -=head1 NAME - -seedGff.pl - -=head1 SYNOPSIS - -% seedGff.pl -i annotation.gff -p BeginPosFromAtg [-l lgSeed | -e EndPosFromAtg ] [-h] - -=head1 DESCRIPTION -This script will parse input gff file and write information in gff3 format. - - -i|--input fileName gff input file name of annotations - -p|--pos BeginPosFromAtg greather positive number for the begin position of the seed from Atg - [-l|--length seedLength] lentgth of the seed to compute (default 4nt) - [-e|--end seedEnd] end of the seed to compute (smaller positive number) - -o|--output fileName gff output file name - [-h|--help] help mode then die - -=head1 AUTHOR - Claire Toffano-Nioche - mar.11 - from Claire Kuchly initial script - -=cut -#----------------------- -my ($inFileName, $beginSeed, $endSeed, $lgSeed, $outFileName) = ("", 0, 0, 0, "SEED.gff") ; - # command line check - foreach my $num (0 .. $#ARGV) { - SWITCH: for ($ARGV[$num]) { - /--input|-i/ && do { - $inFileName=$ARGV[$num+1]; - open (INGFF, "< $inFileName" ) or die "Can't open gff file: \"$inFileName\"\n" ; - last }; - /--pos|-p/ && do { - $beginSeed=$ARGV[$num+1]; - last }; - /--end|-e/ && do { - $endSeed=$ARGV[$num+1]; - last }; - /--length|-l/ && do { - $lgSeed=$ARGV[$num+1]; - last }; - /--output|-o/ && do { - $outFileName=$ARGV[$num+1]; - last }; - /--help|-h/ && do { exec("pod2text $0\n") ; die }; - } - } - open(UTR5,">$outFileName") or die "Error can't $outFileName open for output. $!\n"; - if (($endSeed > 0) and ($lgSeed > 0)) { - print "Error : only -e or -l definition, not both\n"; - exec("pod2text $0\n") ; die ; - } elsif ($lgSeed > 0) { - print "ERROR : Lg Seed => TODO \n"; - } - - #Création des fichiers de filtres (séquences UTR) : - #print "Création des fichiers de séquences !\n"; -###Creer les fichiers des séquences en 5' et 3' des gènes. -###Seed pour les clusters en 5' : il faut qu'ils soient encrés sur le -20 par rapport à l'ATG. Donc seed de -22/-18. - while(my $ligne = <INGFF>){ - chomp($ligne); - my @list = split(/\t/,$ligne) ; - my $finUTR5 ; - my $debUTR5 ; - my $strand = $list[6] ; - if($strand eq "+"){ - $finUTR5 = $list[3]-$endSeed; - $debUTR5 = $list[3]-$beginSeed; - } elsif($strand eq "-"){ - $debUTR5 = $list[4]+$endSeed; - $finUTR5 = $list[4]+$beginSeed; - } - if($debUTR5 < 0){$debUTR5 =0;} - if($finUTR5 < 0){$finUTR5 =0;} - print UTR5 "$list[0]\t$list[1]\t5UTR\t$debUTR5\t$finUTR5\t$list[5]\t$list[6]\t$list[7]\t$list[8]\n"; - } - close INGFF; - close UTR5; -exit(0); |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/seedGff.xml --- a/SMART/bacteriaRegulatoryRegion_Detection/seedGff.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,35 +0,0 @@ -<tool id="seedGff" name="seedGff"> - <description>Creates the seed from -15 to -25 bp before ATG</description> - <command interpreter="perl"> seedGff.pl -i $inputFile -p $startPosFromAtg -e $endPosSeed - #if $optionSeedSize.seedSize == "Yes": - -l $optionSeedSize.seedLength - #end if - -o $outputFile - </command> - <inputs> - <param name="inputFile" type="data" label="Input File" format="gff"/> - <param name="startPosFromAtg" type="integer" value="25" help="greather positive number for the start position of the seed from Atg "/> - <param name="endPosSeed" type="integer" value="15" help="end of the seed (smaller than the sart of the seed, positive number)"/> - <conditional name="optionSeedSize"> - <param name="seedSize" type="select" label="The length of seed." help="If you have choosed the value of start/end position of seed, you don't need to fill this option."> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="seedLength" type="integer" value="4" label="The length of seed, default: 4nt" /> - </when> - <when value="No"> - </when> - </conditional> - - - </inputs> - - <outputs> - <data format="gff" name="outputFile" label="[seedGff] Output File"/> - </outputs> - - <help> - command example: perl seedGff.pl -i input_annot.gff -p 25 -e 15 -o output_cis_seed.gff - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/sortGff.pl --- a/SMART/bacteriaRegulatoryRegion_Detection/sortGff.pl Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,88 +0,0 @@ -#!/usr/bin/perl -w -### -# But : ajout ou modif de couleur d'un gff -# -# Entrees : fichier gff -# -# Sortie : gff affiche a l'ecran -# -###------------------------------------------------------ - -#!/usr/bin/perl -w - -use vars qw($USAGE); -use strict; - -=head1 NAME - -sortGff.pl - sort a gff file - -=head1 SYNOPSIS - -% sortGff.pl -i file.gff [-h] - -=head1 DESCRIPTION -This script will sort a gff file (only when inversion of two successive lines). - - -i|--input fileName gff input file name - -o|--output fileName gff3 output file name - [-h|--help] help mode then die - -=head1 AUTHOR - Claire Toffano-Nioche - mar.11 - -=cut - -#----------------------- -my ($fileName, $colourGff, $outFileName) = ("", "", "sortOut.gff3") ; - # command line check - foreach my $num (0 .. $#ARGV) { - SWITCH: for ($ARGV[$num]) { - /--input|-i/ && do { - $fileName=$ARGV[$num+1]; - open ( fichierGff, "< $fileName" ) or die "Can't open gff file: \"$fileName\"\n" ; - last }; -# /--output|-o/ && do { -# $outFileName=$ARGV[$num+1]; -# last }; - /--help|-h/ && do { exec("pod2text $0\n") ; die }; - } - } - # informations retrieval -# open(OUT,">$outFileName") or die "Error can't $outFileName open for output. $!\n"; - my @lines = <fichierGff> ; - close fichierGff ; - # treatment - #print "gff file read ; number of lines : $#lines\n"; - my $previous = 0; - my $i = 0; - #print "$#lines\n" ; - while ($i <= $#lines) { - my @infos = split('\t', $lines[$i]) ; - #print "info[3]:$infos[3]; prv:$previous!\n"; - if ($infos[3] < $previous) { - &exchange($i, $infos[3]) ; - $previous=$infos[3] ; - $i--; - } - $previous=$infos[3]; - $i++; - } - for (my $i=0 ; $i <= $#lines ; $i++) { -# print OUT $lines[$i] ; - print $lines[$i] ; - } -#close OUT ; -exit(0); -#----------------------- -sub exchange { - my ($index, $position) = @_ ; - my @info_col = split("\t", $lines[$index-1]) ; - if ($info_col[3] > $position) { - #print "$lines[$index]"; - my $line_to_push = $lines[$index-1] ; - $lines[$index-1] = $lines[$index] ; - $lines[$index] = $line_to_push ; - } else { - print "TODO : push > one line\n" ; - } -} |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/sortGff.xml --- a/SMART/bacteriaRegulatoryRegion_Detection/sortGff.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,15 +0,0 @@ -<tool id="sortGff" name="sortGff"> - <description>Sorts a gff file.</description> - <command interpreter="perl"> sortGff.pl -i $inputFile > $outputFile </command> - <inputs> - <param name="inputFile" type="data" label="Input File" format="gff"/> - </inputs> - - <outputs> - <data format="gff3" name="outputFile" label="[sortGff] Output File"/> - </outputs> - - <help> - command example: perl sortGff.pl -i *_unsort.gff3 > *_sort.gff3 - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.pl --- a/SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.pl Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,189 +0,0 @@\n-#!/usr/bin/perl -w\n-###\n-# Main : defining utr and intergenic operonic intervalles from a transcripts file following a referencies file \n-# \n-# Input : 2 gff files to intersect, transcript queries vs referencies\n-#\n-# Output : resulting gff file printing to standard output\n-#\n-###------------------------------------------------------\n-use vars qw($USAGE); \n-use strict; \n-\n-=head1 NAME\n-\n-splitTranscriptGff.pl - compare 2 input gff files and define utr and intergenic operonic intervalles by couple of overlapping elements\n-\n-=head1 SYNOPSIS\n-\n-% intervallsExtractorGff.pl -i referencies.gff -j transcriptQueries.gff -s strand [-h] \n-\n-=head1 DESCRIPTION\n-This script will intersect 2 gff files and compute distance between 2 successives lines. Take care both of sorting by positions the input files and of that referencies are included in transcriptQueries.\n-\n- -i|--input1 fileName gff input file name: included elements\n- -j|--input2 fileName gff input file name: extended elements\n- [-s|--strand] [s|d]\t s for single strand (colinear) or d for double strands (antisense) [default d]\n- [-h|--help] help mode then die \n-\n-=head1 USECASE\n-Define many fragments for each extended element (transcript): UTR5, gene, UTR3, "inOperon" for intergenomic region between 2 genes\n-intervallsExtractorGff.pl -i CDSannotations.gff -j RNAseqTranscripts.gff > UTRsGenesOperonsLists.gff;\n-\n-=head1 KWON BUGS\n-No disjonction of overlapping elements of the included elements (-i file).\n-In usecase, overlapping genes are fused in one long gene.\n-\n-=head1 AUTHOR\n-Claire Toffano-Nioche - sep.11\n-\n-=cut\n-#-----------------------\n-sub feedPositionTab { my ($val, $pF, $pB, @info) = @_ ;\n-\t\t#print "feedPositionTab::$#info, ", ($#info+1)/4," \\n";\n-\tfor (my $i=0 ; $i <= $#info ; $i+=4) { # for each extended element \n-\t\t\t#print "....$info[$i+2]\\n";\n-\t\tif ($info[$i+3] =~ /\\+/) {\n-\t\t\tfor (my $c = $info[$i+1] ; $c <= $info[$i+2] ; $c++) { @$pF[$c]=$val } ; # sequence Forward\n-\t\t} else {\n-\t\t\tfor (my $c = $info[$i+1] ; $c <= $info[$i+2] ; $c++) { @$pB[$c]=$val } ; # sequence Backward\n-\t\t}\n-\t}\n-\t\t#print "feedPos...:: ", join(".", @$pF[0..100]), "\\n";\n-\t\t#print "feedPos...:: ", join(".", @$pB[0..100]), "\\n";\n-}\n-#-----------------------\n-sub recupInfo {\tmy ($pInfo, @lines) = @_ ;\n- for (my $i=0 ; $i <= ($#lines+1)*4-1 ; $i+=4) {\n- \tmy @line = split("\\t",$lines[$i/4]);\n-\t\tpush(@$pInfo, $line[0], $line[3], $line[4], $line[6]) ; # 0=nom, 3=debut, 4=fin, 6=sens\n-\t}\n-\t#print "recupInfo::fin=", ($#lines+1)*4, "\\n" ;\n-}\n-#-----------------------\n-sub tagName { my ($seqN, $posB, $posE, $strand) = @_ ; \n-\tmy $tagN=$seqN.$strand.$posB."..".$posE;\n-\t\t#print "tagName:",join("_",@_)," et tagName:$tagN\\n";\n-return $tagN;\n-}\n-#-----------------------\n-sub transitionAnalysis {\n-my ($pos, $seq, $s, $pdebAmont, $pfinAmont, $pdebIn, $pfinIn, $pdebAval, $pfinAval, $ptag) = @_ ;\n-\tmy $enCours = 0 ; my $precedant = 0 ;\n-\t$enCours = @$ptag[$pos] ; \n-\t$precedant = ($s =~ /\\+/?@$ptag[$pos-1]:@$ptag[$pos+1]) ; \n- if ($enCours ne $precedant) {\n- \t#print "transi...:: $s, $pos, $precedant, $enCours\\n";\n- \t#print "transition::$$pdebAmont, $$pfinAmont, $$pdebIn, $$pfinIn, $$pdebAval, $$pfinAval\\n";\n- \tSWITCH: for ($precedant.$enCours) {\n- \t/01/ && do { $$pdebAmont = $pos ; last SWITCH ;};\n- /02/ && do { $$pdebIn = $pos ; last SWITCH ;};\n- /10/ && do { $$pfinAval = ($s =~/\\+/?$pos-1:$pos+1) ; \n- \t\tif (($s =~ /\\+/)and ($$pdebAval!=$$pfinAval)) {\n- \t\t\tprintf "%s\\tsplit\\tutr3\\t%s\\t%s\\t.\\t%s\\t.\\tName=%s;\\n", \n- \t\t\t\t$seq, $$pdebAval, $$pfinAval, $s, &tagName($seq, $$pdebAval, $$pfinAval, $s) ; \n- \t\t\t#if ($$pdebAval==$$pfinAval) { print "transition 10 +\\n"};\n- \t\t} elsif ($$pfinAval!=$$pdebAval) {\n- \t\t\tprintf "%s\\tsplit\\tutr3\\t%s\\t%s\\t.\\t%s'..b'==$$pdebAmont) { print "transition 12 -\\n"} ;\n- \t\t}\n- \t\t$$pdebAmont = 0 ; $$pfinAmont = 0 ;\n- \t\tlast SWITCH ;\n- \t };\n- /20/ && do { $$pfinIn=($s =~/\\+/?$pos-1:$pos+1) ; \n- if (($s =~ /\\+/) and ($$pdebIn!=$$pfinIn)) {\n- \tprintf "%s\\tsplit\\tgene\\t%s\\t%s\\t.\\t%s\\t.\\tName=%s;\\n", \n- \t\t\t\t$seq, $$pdebIn, $$pfinIn, $s, &tagName($seq, $$pdebIn, $$pfinIn, $s) ; \n- \t\t} elsif ($$pfinIn!=$$pdebIn) {\n- \t\t printf "%s\\tsplit\\tgene\\t%s\\t%s\\t.\\t%s\\t.\\tName=%s;\\n", \n- \t\t\t\t$seq, $$pfinIn, $$pdebIn, $s, &tagName($seq, $$pfinIn, $$pdebIn, $s) ; \n- \t\t}\n- \t\t$$pdebIn = 0 ; $$pfinIn = 0 ;\n- \t\tlast SWITCH ;\n- \t };\n- /21/ && do { $$pdebAval=$pos ; $$pfinIn=($s =~/\\+/?$pos-1:$pos+1) ; \n- if (($s =~ /\\+/) and ($$pdebIn!=$$pfinIn)) {\n- \tprintf "%s\\tsplit\\tgene\\t%s\\t%s\\t.\\t%s\\t.\\tName=%s;\\n", \n- \t\t\t\t$seq, $$pdebIn, $$pfinIn, $s, &tagName($seq, $$pdebIn, $$pfinIn, $s) ; \n- \t\t} elsif ($$pfinIn!=$$pdebIn) {\n- \t\t\tprintf "%s\\tsplit\\tgene\\t%s\\t%s\\t.\\t%s\\t.\\tName=%s;\\n", \n- \t\t\t\t$seq, $$pfinIn, $$pdebIn, $s, &tagName($seq, $$pfinIn, $$pdebIn, $s) ; \n- \t\t}\n- \t\t#$$pdebIn = 0 ; $$pfinIn = 0 ;\n- \t\tlast SWITCH ;\n- \t };\n- }\n- }\n- }\n-#-----------------------\t\n-my ($fileNameI, $fileNameE, $strand) = ("", "", 0) ;\n-# command line check\n-foreach my $num (0 .. $#ARGV) {\n- SWITCH: for ($ARGV[$num]) {\n- /--input1|-i/ && do { \n-\t\t\t$fileNameI=$ARGV[$num+1]; \n-\t\t\topen ( fichierGffI, "< $fileNameI" ) or die "Can\'t open gff file: \\"$fileNameI\\"\\n" ; \n-\t\t\tlast };\n-\t/--input2|-j/ && do { \n-\t\t\t$fileNameE=$ARGV[$num+1]; \n-\t\t\topen ( fichierGffE, "< $fileNameE" ) or die "Can\'t open gff file: \\"$fileNameE\\"\\n" ; \n-\t\t\tlast };\n- /--strand|-s/ && do { \n-\t\t\tif ($ARGV[$num+1] eq "s") { $strand=1}; \n-\t\t\tlast };\n- /--help|-h/ && do { exec("pod2text $0\\n") ; die };\n- }\n-}\n-# memory declarations:\n-my @infoI ; my @infoE ;\n-my $seqName ;\n-my @tagF ; my @tagB ; # Forward and Backward sequence\n-# data retrieval:\n-my @linesI = <fichierGffI> ; my @linesE = <fichierGffE> ;\n-close fichierGffI ; close fichierGffE ;\n-\t\t#print "gff files read ; number of lines : $#lines1 + $#lines2\\n";\n-\t\t# positions management\n-&recupInfo(\\@infoI, @linesI) ;\n-&recupInfo(\\@infoE, @linesE) ;\n-# treatement: \n-# transform gff lines into chromosomal position tags : 0 for nothing, 1 resp. 2 for extended resp. included elements\n-if (($#infoI) and ($#infoE)) { \n-\t$seqName=$infoI[0] ;\n-\t\t#print "fin : $infoE[$#infoE-1]\\n";\n-\tfor (my $i=0 ; $i <= $infoE[$#infoE-1] ; $i++) { $tagF[$i] = 0 ; $tagB[$i] = 0 ; } ; # "O" tag in all chr. positions\n-\t\t#print "seqName : $seqName\\n" ;\n-\t&feedPositionTab(1, \\@tagF, \\@tagB, @infoE) ; # "1" tag for all extended elements\n-\t&feedPositionTab(2, \\@tagF, \\@tagB, @infoI) ; # "2" tag for all included elements\n-\t\t#print join("", @tagF), "\\n";\n-\t\t#print join("", @tagB), "\\n";\n-\t# transition management:\n-\tmy ($beginUpstream, $endUpstream, $beginIncluded, $endIncluded, $beginDownstream, $endDownstream) \n-\t\t= (0, 0, 0, 0, 0, 0) ;\n-\tfor (my $i=1 ; $i <= $#tagF-1 ; $i+=1) {\n-\t\t&transitionAnalysis($i, $seqName, "+", \\$beginUpstream, \\$endUpstream, \\$beginIncluded, \\$endIncluded, \\$beginDownstream, \\$endDownstream, \\@tagF) ;\n-\t}\n-\t($beginUpstream, $endUpstream, $beginIncluded, $endIncluded, $beginDownstream, $endDownstream) = ($infoE[$#infoE-1], $infoE[$#infoE-1], $infoE[$#infoE-1], $infoE[$#infoE-1], $infoE[$#infoE-1], $infoE[$#infoE-1]) ;\n-\tfor (my $i=$#tagB-1 ; $i >= 1 ; $i-=1) {\n-\t\t&transitionAnalysis($i, $seqName, "-", \\$beginUpstream, \\$endUpstream, \\$beginIncluded, \\$endIncluded, \\$beginDownstream, \\$endDownstream, \\@tagB) ;\n-\t}\n-}\n-exit(0) ;\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.xml --- a/SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,21 +0,0 @@ -<tool id="splitTranscriptGff" name="splitTranscriptGff"> - <description> Define UTRs and intergenic operonic regions from a transcript file and following a reference file </description> - <command interpreter="perl"> - splitTranscriptGff.pl -i $referenciesFile -j $transcriptsFile > $outputFile - </command> - - <inputs> - <param name="referenciesFile" type="data" label="Referencies Input File" format="gff" /> - <param name="transcriptsFile" type="data" label="Transcripts Input File" format="gff" /> - </inputs> - - <outputs> - <data format="gff3" name="outputFile" label="[splitTranscript] Output File"/> - </outputs> - - <help> - Note that iputs files should be sorted by increasing positions and that expressed referencies should be included in transcripts. - - Command example: perl splitTranscriptGff.pl -i annotations.gff -j transcripts.gff > TUTag.gff3 - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/strictlyIncludeGff.pl --- a/SMART/bacteriaRegulatoryRegion_Detection/strictlyIncludeGff.pl Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,79 +0,0 @@ -#!/usr/bin/perl -w -### -# But : protocol permettant la detection d'RNA non codant potentiel -# -# Entrees : fichier de mapping Smart gff3 -# fichier gff des gènes -# fichier gff des clusters Cis regulateur potentiel -# -# Sortie : fichier gff des clusters ARN nc -# -###------------------------------------------------------ - -use vars qw($USAGE); -use strict; - -=head1 NAME - -protocol_NC_V2_CTN3.pl - -=head1 SYNOPSIS - -% strictlyIncludeGff.pl -i toSelect.gff3 -t template.gff3 > result.gff3 - -=head1 DESCRIPTION - -strictlyIncludeGff.pl - print elements strictly include in template (gff files) - - -i|--input fileName gff input file name - -t|--template fileName gff template file name - [-h|--help] help mode then die - -=head1 AUTHOR - CTN - mar.11 -(from RNA-Vibrio/protocol_NC_V2_CTN3.pl - Claire KUCHLY) - -=cut - -#---------------------------------------------------------------------------- -# check command line : -my $outFileName = "outSIG.gff3"; -if ($#ARGV==0) { - die (exec("pod2text $0\n")); -} else { - foreach my $num (0 .. $#ARGV) { - SWITCH: for ($ARGV[$num]) { - /--input|-i/ && do { open(ARN,"<$ARGV[$num+1]") - or die "Error: Can't open \"$ARGV[$num+1]\", $!"; - last }; - /--template|-t/ && do { open(SEED,"<$ARGV[$num+1]") - or die "Error : Can't open file \"$ARGV[$num+1]\", $!"; - last }; - /--help|-h/ && do { exec("pod2text $0\n") ; die }; - } - } - ##NC_011753.2 RefSeq gene 367 834 . - . locus_tag=VS_0001;db_xref=GeneID:7162789 -# open(OUT,">$outFileName") or die "Error can't $outFileName open for output. $!\n"; - my @seed ; - my $s=0; - while (my $seedLine = <SEED> ) { - my @list = split(/\t/,$seedLine); - $seed[$s][0]= $list[3] ; # position begin seed - $seed[$s][1]= $list[4] ; # position end seed - $seed[$s][2]= $list[6] ; # seed sens - $seed[$s][3]= $list[0] ; # chromesome name - $s++; - } - close SEED ; - while(my $ligne = <ARN>){ - $s=0; - my @list = split(/\t/,$ligne); - while (($s <= $#seed)) { - if (($seed[$s][3] eq $list[0]) and ($seed[$s][0] <= $list[3]) and ($seed[$s][1] >= $list[4]) and ($seed[$s][2] eq $list[6])) { # if list include in seed + same direction - print "$ligne"; - } - $s++; - } - } - close ARN ; - exit(0); -} |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/strictlyIncludeGff.xml --- a/SMART/bacteriaRegulatoryRegion_Detection/strictlyIncludeGff.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,17 +0,0 @@ -<tool id="strictlyIncludeGff" name="strictly include Gff"> - <description>Prints the elements which are strictly included in the template.</description> - <command interpreter="perl"> strictlyIncludeGff.pl -i $inputFile -t $template > $outputFile - </command> - <inputs> - <param name="inputFile" type="data" label="Input File" format="gff"/> - <param name="template" type="data" label="template File" format="gff"/> - </inputs> - - <outputs> - <data format="gff3" name="outputFile" label="[strictlyIncludeGff] Output File"/> - </outputs> - - <help> - command example: perl strictlyIncludeGff.pl -i toSelect.gff3 -t template.gff -o result.gff3 - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/writeResToHTML.py --- a/SMART/bacteriaRegulatoryRegion_Detection/writeResToHTML.py Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,124 +0,0 @@ -#! /usr/bin/env python - -import optparse, os, shutil -from optparse import OptionParser - - -def image(text, url): - return "<center>%s</center><img src='%s'>" % (text, url) - - -def __main__(): - description = "Write all results in one HTML file." - parser = OptionParser(description = description) - parser.add_option("", "--input1Gff1", dest="input1Gff3_1", action="store", type="string", help="First gff3 result in the first analyse.(TRANS detection)") - parser.add_option("", "--input1Gff2", dest="input1Gff3_2", action="store", type="string", help="Second gff3 result in the first analyse. (TRANS detection)") - parser.add_option("", "--input1PNG1", dest="input1PNG1", action="store", type="string", help="PNG (getSize) result in the first analyse. (TRANS detection)") - parser.add_option("", "--input1PNG2", dest="input1PNG2", action="store",type="string", help="PNG (plot) result in the first analyse. (TRANS detection)") - parser.add_option("", "--input2Gff1", dest="input2Gff3_1", action="store", type="string", help="First gff3 result in the second analyse. (ANTISENSE detection)") - parser.add_option("", "--input2Gff2", dest="input2Gff3_2", action="store", type="string", help="Second gff3 result in the second analyse. (ANTISENSE detection)") - parser.add_option("", "--input2PNG1", dest="input2PNG1", action="store", type="string", help="PNG (getSize) result in the second analyse. (ANTISENSE detection)") - parser.add_option("", "--input2PNG2", dest="input2PNG2", action="store", type="string", help="PNG (plot) result in the second analyse. (ANTISENSE detection)") - parser.add_option("", "--input3Gff1", dest="input3Gff3_1", action="store", type="string", help="First gff3 result in the third analyse. (CIS detection)") - parser.add_option("", "--input3Gff2", dest="input3Gff3_2", action="store", type="string", help="Second gff3 result in the third analyse. (CIS detection)") - parser.add_option("", "--input3PNG1", dest="input3PNG1", action="store", type="string", help="PNG (getSize) result in the third analyse. (CIS detection)") - parser.add_option("", "--input3PNG2", dest="input3PNG2", action="store", type="string", help="PNG (plot) result in the third analyse. (CIS detection)") - parser.add_option("", "--outHTML", dest="outHTML", action="store", type="string", help="An HTML output.") - parser.add_option("", "--outImgDir", dest="imgDir", action="store", type="string", help="Copy all result images into imgDir, for Galaxy option.") - (options, args) = parser.parse_args() - - - if not os.path.exists(options.imgDir): - os.makedirs(options.imgDir) - - shutil.copy(options.input1PNG1, options.imgDir) - shutil.copy(options.input1PNG2, options.imgDir) - shutil.copy(options.input2PNG1, options.imgDir) - shutil.copy(options.input2PNG2, options.imgDir) - shutil.copy(options.input3PNG1, options.imgDir) - shutil.copy(options.input3PNG2, options.imgDir) - - - outfile=open(options.outHTML, "w") - #print >>outfile, "<html><head><title>The results for ncRNAs detections.</title></head><body>" - print >>outfile, "<h1><center>The results for ncRNAs detections.</center></h1>" - - #write results for the first analysis - print >>outfile, "<B><center><font color=red size=4>The results of intergenic sRNAs detection.(TRANS)</font></center></B>" - print >>outfile, "<center><strong>The results of comparison to already known ncRNA to validate some candidates.</strong></center><p>" - input1Gff1 = open(options.input1Gff3_1, "r") - lines = input1Gff1.readlines() - input1Gff1.close() - for line in lines: - print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line - print >>outfile, "<p>" - print >>outfile, "<center><strong>The results of comparison to already known ncRNA to see which ncRNAs are not detected.</strong></center><p>" - input1Gff2 = open(options.input1Gff3_2, "r") - lines = input1Gff2.readlines() - input1Gff2.close() - for line in lines: - print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line - print >>outfile, "<p>" - img_input1PNG1 = os.path.basename(options.input1PNG1) - image1=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input1PNG1) - print >>outfile, "%s" % image1 - print >>outfile, "<p>" - img_input1PNG2 = os.path.basename(options.input1PNG2) - image2=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input1PNG2) - print >>outfile, "%s" % image2 - print >>outfile, "<BR><p>" - - - #write results for the second analysis - print >>outfile, "<B><center><font color=red size=4>The results of asRNAs detection.(ANTISENSE)</font></center></B>" - print >>outfile, "<center><strong>The results of comparison to already known ncRNA to validate some candidates.</strong></center><p>" - input2Gff1 = open(options.input2Gff3_1, "r") - lines = input2Gff1.readlines() - input2Gff1.close() - for line in lines: - print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line - print >>outfile, "<p>" - print >>outfile, "<center><strong>The results of comparison to already known ncRNA to see which ncRNAs are not detected.</strong></center><p>" - input2Gff2 = open(options.input2Gff3_2, "r") - lines = input2Gff2.readlines() - input2Gff2.close() - for line in lines: - print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line - print >>outfile, "<p>" - img_input2PNG1 = os.path.basename(options.input2PNG1) - image1=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input2PNG1) - print >>outfile, "%s" % image1 - print >>outfile, "<p>" - img_input2PNG2 = os.path.basename(options.input2PNG2) - image2=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input2PNG2) - print >>outfile, "%s" % image2 - print >>outfile, "<BR><p>" - - - #write results for the third analysis - print >>outfile, "<B><center><font color=red size=4>The results of long 5'UTRs detection.(CIS)</font></center></B>" - print >>outfile, "<center><strong>The results of comparison to already known ncRNA to validate some candidates.</strong></center><p>" - input3Gff1 = open(options.input3Gff3_1, "r") - lines = input3Gff1.readlines() - input3Gff1.close() - for line in lines: - print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line - print >>outfile, "<p>" - print >>outfile, "<center><strong>The results of comparison to already known ncRNA to see which ncRNAs are not detected.</strong></center><p>" - input3Gff2 = open(options.input3Gff3_2, "r") - lines = input3Gff2.readlines() - input3Gff2.close() - for line in lines: - print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line - print >>outfile, "<p>" - img_input3PNG1 = os.path.basename(options.input3PNG1) - image1=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input3PNG1) - print >>outfile, "%s" % image1 - print >>outfile, "<p>" - img_input3PNG2 = os.path.basename(options.input3PNG2) - image2=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input3PNG2) - print >>outfile, "%s" % image2 - print >>outfile, "<BR><p>" - - -if __name__=="__main__": __main__() |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/bacteriaRegulatoryRegion_Detection/writeResToHTML.xml --- a/SMART/bacteriaRegulatoryRegion_Detection/writeResToHTML.xml Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,36 +0,0 @@ -<tool id="writeResToHTML" name="writeResToHTML"> - <description>Write all ncRNAs analysis results into an HTML file (Only for ncRNAs analysis pipeline).</description> - <command interpreter="python"> writeResToHTML.py - --input1Gff1 $input1GffFile1 --input1Gff2 $input1GffFile2 --input1PNG1 $input1PNGFile1 --input1PNG2 $input1PNGFile2 - --input2Gff1 $input2GffFile1 --input2Gff2 $input2GffFile2 --input2PNG1 $input2PNGFile1 --input2PNG2 $input2PNGFile2 - --input3Gff1 $input3GffFile1 --input3Gff2 $input3GffFile2 --input3PNG1 $input3PNGFile1 --input3PNG2 $input3PNGFile2 - --outHTML $outHTML - --outImgDir $outHTML.files_path - 2> $log </command> - - <inputs> - <param name="input1GffFile1" type="data" label="First gff3 result in intergenic sRNAs analysis. (TRANS detection) " format="gff3"/> - <param name="input1GffFile2" type="data" label="Second gff3 result in intergenic sRNAs analyse. (TRANS detection) " format="gff3"/> - <param name="input1PNGFile1" type="data" label="PNG (getSize) result intergenic sRNAs analyse.(TRANS detection)" format="png"/> - <param name="input1PNGFile2" type="data" label="PNG (plot) result in intergenic sRNAs analyse. (TRANS detection) " format="png"/> - - <param name="input2GffFile1" type="data" label="First gff3 result in asRNAs analysis. (ANTISENSE detection) " format="gff3"/> - <param name="input2GffFile2" type="data" label="Second gff3 result in asRNAs analyse. (ANTISENSE detection) " format="gff3"/> - <param name="input2PNGFile1" type="data" label="PNG (getSize) result asRNAs analyse.(ANTISENSE detection)" format="png"/> - <param name="input2PNGFile2" type="data" label="PNG (plot) result in asRNAs analyse. (ANTISENSE detection) " format="png"/> - - <param name="input3GffFile1" type="data" label="First gff3 result in long 5'UTRs analysis. (CIS detection) " format="gff3"/> - <param name="input3GffFile2" type="data" label="Second gff3 result in long 5'UTRs analysis. (CIS detection) " format="gff3"/> - <param name="input3PNGFile1" type="data" label="PNG (getSize) result in long 5'UTRs analysis. (CIS detection) " format="png"/> - <param name="input3PNGFile2" type="data" label="PNG (plot) result in long 5'UTRs analysis. (CIS detection) " format="png"/> - - </inputs> - - <outputs> - <data format="HTML" name="outHTML" label="[writeRes2HTML] Output HTML File" help="This output file shows all results by ncRNAs detection analysis."/> - <data format="txt" name="log" label="[writeRes2HTML] Output log File"/> - </outputs> - - <help> - </help> -</tool> |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/REF.fasta --- a/SMART/data/REF.fasta Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,33148 +0,0 @@\n->C10HBa0111D09_LR276\t15142\t24441\t|Longueur=9300\n-GAACAAACAACCCCTTTTTGGAGGTGTTGGCGCGTCGTGCAGCTTACACTCAAAAGTTAA\n-AAAGTTGCCTTGCGATGCGGTCATGTTACAAACCTCTCTGCCTTAAATTAAATTCCATAA\n-CCAAGATTTGGAGGTGCCTCAACGATGCGCAGCCATGTCCCATATTTGGTCGCCTCGTTT\n-AAAAGTCAAGTTAGACTTAATTAAGAGGTCCAACTAGTGTAGGGGCGTTTTGAGTACTTG\n-TGGGATTTATTATAAACGGTTTTGAGTCACTTTAAACCCACTTCACCAATTAAAACAAAA\n-TCCTCAAGTTAAAACTCAATATCTTTCCATTCTCTCTCTCTAAAACCTTCATTGGAGATA\n-TTTGAAGCTCCACGGAAGAAGGTTAATTTTCCAAGGTTTCAATGAAAATTTCGTGTATAG\n-GTCTTCAATAAGGTATGGTGATTTCATCCTTGATTCTTCTATCATTCAAGGATCCAATTC\n-AAAGGTTTTTCAAAAGATCTCAAAAATCCTATTTCGAATTCTAAGTATGGGTTCTTCCAT\n-TTAAAGGTTTAAATGGATGAATTATGATGTTTTCAATGTTAGTTGATGTTTTTATGATAA\n-AAAAACTCCATGAACCCATGAGCATCCTAATTCTCTAATTTTGTCTTGTAAATTGAGTTT\n-GATAATTGTGATTGGTTATGGATGGAATTGTATTTAGATTGCTCTATATTGTTGATTCTT\n-ATTGTTAACCTATCTCTATATATGTAGAATTGAGATTGTAAGGATGAGTTAGTAATCTTG\n-GCTTTATGGGCTTTCGAATCCGGGTTTACCCCCTGGATGTAACCGGCATCCTCGCCCTTT\n-TTCAAGGACTAAGACCAACCTTTTAGTCTCATGTCATTACATTCATAGGTTGACAAATGC\n-GGAAAAATTTAAAACTTTCATTATCACTACTTGGAGGTTTACATAGACCTCTACATACAC\n-ATAAGATATATTCATATAGAGTATACATAGACCCTTCGTATAGGAAGGTTACATAGCCAT\n-CTACTTTTATTACACATACATATATATAAAATATAAAAATAGTCTAACGATTGTCTCATC\n-TCATACCCTCTAAACGATTATCACAATATGGGCATAACCCTTACATCAATCAAACAAGAG\n-CACATATAGGTCATACAAAAGTATAGTACTCAATTAAAAAGGAAAGAAATGAAAGAGTCT\n-TTAAGCTCATAACAAGTCCATAAGCTAGATTATGGCATTGACCTCAAAAGTTGAGGACCT\n-TATGTGCGTACACAAGCAAAACATGCTAAAAAGGGACTTTTTAGTCAAAACATGCCCATT\n-TATCCCTTTAAGAACCTACTACAAAGCCAACAAGTCATACCAACCAACCAAACATGCTTA\n-CTATCTCAACAAGTAATACTTATCCCAACATACTTGAAACCATGATTTACTACAACCCTA\n-TCACCAAGGAAAAATATCACAAGAATGAATAAGAGTCAATCATATCATGATAGAGAGACA\n-ACTATTCATGAATCCTTATCAACTCAACAAGTGCAATAACCAAGCAAAGCCTCATAACCT\n-TACTCAATCAAGTATCCTCAAAAAGAAACCATGACCAATGTCCAACTTTACCTAACATAG\n-CATTTAGGTTTACATTTTATCATATATTAACATTATGACCCAAGGCATACTCATTAGTAA\n-ACTAATTAATATATAATATCAACAATGTGCCATAGTAATCATATATACATAATATATCAT\n-CATAACATAAACATATATAAAAACCTCCTTCTAAGACTCCCCTCAAGGCTAACTAGTGAA\n-ATGTTTAGGTAGAGCCCCATACCCCTACCTAGATTAAGCTAGACCCCTTAGGTTATCCAA\n-GTTAGAGTTCAAGTCCTTTAATTCGTTTTACCTTTTGGGAACATCTTGCCCTAACCGACA\n-TAGACCACATGAGCTAGTGTGGGATACGGTTCCAAAAAACCCTACACAGAAAGAAGGCGG\n-ACTACTTGCCAAAGTATTACCAAAACATGAAACATAGCAACTACGTTGATCCACTAGCAA\n-GTATTTCTATAGGGGCAACATAGTTCAAGAACTCTGAGATATACTTGAGACCCTCTTTAT\n-GCGCCATGCATTATAGTCTCCAACCTCAAGAGTAATGTAGTGTTCCTACCTTCCCCATGT\n-GAGAAAGGACACTCCTCAATCTAGTTCACTCGGTGCTAAGCTAGAGACCCTTTTTGAAAT\n-GTCTTTAAGCCTTTAATTATCAATCATAGCTTAGCTTAGGTCATAGGGTATATCTCTTGT\n-ATAATCATCATCATCAATAGCTCAATAATAATTGTATGAGTATAAGTCCTTTCATCACAA\n-TTCATATAAGTGAGGTTAACATGTTAGCATTTCATTGCATATCAAGAAACATTGATGATT\n-CTTACCATCCTTGTATCACATACACCTTAATCAATCTCACAACATAGTCAGGACATATCA\n-ATTCAACATCATACCACCCTATAATCCTAATATAAGGCATACTCCAATATAACTTCACGT\n-CTTAACAAAAATTTATCACAATTGGAATTAAAGATAGAGATTCTAAGACTTAACAAGTCT\n-TCCTTGTAGTTCATCATCAAGGTCTTACCATCAACCCATAACTCAACCAAGTTTGGGGAG\n-TAACATCATCACACAATGATAATCAATAGGATAACAAGGCTAATTTCATCTCTATAACAC\n-AATTCAACACTAGATCATAACTTAAGACAAGATACATAGGCTAATTTCACACTATAATTC\n-ATAACCTAAATCACATCTCAAGAAATAGCATTATAGTCCTATAATTCATATTAATTTGTT\n-CATAATAACACAATAGGATAGTAATTTAATCAATAACCAAGTCAATTGAATGATCACAAT\n-ACAATATACATCAATATCACAAGCTAGGGTTAGGGATGAAGGATCATATTCTTCAATTTA\n-GACCAAACCACTAACAATTACCATAATAAAGTTTAAATTCATGTAAATGTATTCAATATA\n-ACCTAAATAAATCATTAACAACTCAATCCATAACTTCAATTTCGTAATTGAATGAAACCC\n-ATAAGAAAATTCACCTTTTGAAATCCATTTTAAAGAAACCCTTTGAGGAAAGAGCCTCAA\n-AGGTGAATTAGATCCCATATATTAATGTTTGATGATGAATTCGCCCCTTTCCATCCCCCA\n-AACCCTTATCCTTGCTAGTTTTTAATGGTGAGTTCAAGTAGAGAGAGAAATAAGAGAGAA\n-GGAAGAGAGTTTTTGTCTTAGAGTTCTAATTAATTTAATTGGGGTTGGGGATTTTATATG\n-CGTTTTAAGTTAGTTAATTAGTCACCCCTCAATACCTAACTAACCCCTGAACCACCTAAT\n-TAATTAAATGAATCAATATAAAAACATACAGGAAATTTGACCTTCACAGACGAGACCCCG\n-AACGACGGGCCATCTGTGAGTCAACGGTCCCTCACCCCTCCGTCCTGCACTCTATCGATC\n-AGTTCATAGACTGTGCAGGCAGATCAATTCTTCAACTTGTCTAAGTATGGGATGACGGTG\n-GTATCGACTCCCCGTCAGTCCACACACGGACCGTAGGTGGTCCCATCGATGCGCATTGTC\n-TAGTCCTTGTTTGTTCAAACACAAGGGCCTCAAGGGCCCTTGGTTGGTGCTTGGGGAGTC\n-GTACCCATACGTTTCAATCATGAAACAACTCAAAAACCTATAATCTATCCTTCCACCAAT\n-TTTTGTACCTTTCCGACTCTTAAAAGGTAGTCAAATAGGCTAAGGCACGCTAACACCCCT\n-TTGAACCAACTTCCTGGACGTTC'..b'CAATATTCCATATTGATCGCCAGCTTCCATTGCTACAAAAGA\n-TGCATATAGTATCAGCTTCTTTAGACAAAGCTATAAGAAGTATCAGTTGACCCAATTGAC\n-AAGTCACACGTGCTATAACAAGATATCACTTGACGCAAGTGACAAGTGTGAAGCTGACAG\n-GAAAATAGGCAATAGAATCCCTCATTCTTTGTTTATATATAGCAACCTATTACTTCAGTA\n-TCTGTTTACAAGTTCTGCACCACGATAAGTATAACTATTTAGAAATTATGAAGGGAGTGT\n-TGCACAAATTAGTCAGGGTTAGAATTTTAATAATCCAACACACCAGAAATTCTGAGGACT\n-ATGCCTAGCAGCTGAAATCACCACAACAAGTTCAAAGTCAAATCCTGGCTCTTCCACATC\n-CTTTCCCTTCGTACAGTAAACTGAACAGATGCCTTTTGGATATGTTTCACTCACATACTT\n-CATAATTTCAGCATCCATGGCAGACCTACACAAGAATTACCATGAATAGGAGAATTTGGC\n-AAGCAACGGTAATCACAAAGTCAGTACTCATAAACCAAGCCTCTGATGAGAAGAACTAAC\n-CATGTTAAGAAGGGAACTACTCACATAAAACAAAAACATGATTTTTATAATCTGCATGCC\n-AAGCATTAGGAACTATTGAAGAATTCACTGCGATCTCAGAATATAATCCTTTCATACTCT\n-TAATGCCTCCCAATTATACCAAATTTAGGTGTCTTACTACCATTTTAGTATCTGACATTG\n-ATGTCATTACCCATTAATTTGGAGACACTGGTTCCTCACCGATAAAGATGAACAAAAAGG\n-TAAACCAGTGTATTATGAATCAGATCTCTTTATGGAATAAAAACACACATGAATCATGAT\n-GTAGGATCTTATTAACACTTGAGGACTGAGGCGAAGATTACTAAGAATATCCCGAAAGAT\n-AAGACATAGAATGTAATATAGAAGGACAGAGAACAAATGATACTGATTAAGAAGAAGAGC\n-ATCTATATAGGAGAGATTAGCCTAAACTATTTATTTTCAGACTGATTTCGGTGAGCGCAG\n-ACCAAAACATGCAGCTTTTTTTTCAATTAAGCCGGAAAGACAATTTCCACAAGAAATGCA\n-ACTGTTCTAGCATATCTTAAACTATAATCTGAGTGCTGTCTGAGAACTGAGGTTGAATTT\n-GCAAGTCTTGTTGAGCATGGTTAAAAAATAAGTCCAATTAGGCAAAATAATTGTGAATGT\n-CATAATATAGAAGAACTTCAACATCTCAATGGGAAAAACAGAAAGTGAGTAGCTAAAAAG\n-GGGAGCAATACCAAAGATATTAAACTGAGAAATATATCTCATACCCTACAGATGCATACC\n-TATACTCTTCCACGAAAGCAGATGGAAGTTCTTCATCTCTTGCTGGCCTAACGTCTTTAC\n-AAACCTAGAATGCAGACATACCATGAGCTTACAAGAAGGGAGCATAAATTATTACACGGC\n-AACAATAACTAGGAAAAAAAGAGAGAGAGGAAATACATTTAATTTCACAGCCCTTGAATT\n-ATGAATAAAACCATGCACTTGTTATATTAAGCAGAGACTACTTCCACTTTTCCAATCTAT\n-TTACATCTACTTCATCACATTAACAAGAATAGAAAAGAAATGCATGTTATGTGACATTCA\n-GCACTGTAGACTAATGAGGATTAATTTACAACCATGGACCAGCTATAGCAGAAGAGACCT\n-TATTTTACTTTTCCAAAATTGGTATTTACTCCATCACCATTAACAAGAATAAAAAATGCA\n-TCTTATGTGAAGTTCATAACTATTGAATAATGAGGTTAATCAAGAGCTTGCTATATCAAA\n-GCACATTTTTCAAGTTTACAATTTCTTCATTCTTGGTATCCACTTCTATCATGAAAACCA\n-ACCTAACAGTTAACACAATTCACTCTGGTGTTTTGTTCTTTATCCCTAATGCCTGAGTGT\n-GTTTAACTAATCAAGTTCCAATCAGCCAGAAGATGTCTAAACATACTAAACTATAGATAA\n-ACAACATGAGCATAAAACCAGTTTATGTAGAGATTTTTAATTGCACAGCATAAAAAGGAG\n-TACCCCCGGCACTATATGTGCTTCTCTTTCTTTTTTTCTTACTTCGTCCTGATCTTTTTA\n-CTTTTCTTTTCCTTTCTTTCAGAATAAGCACATTTTTGGATATAGTCCCACCATCTCTAC\n-CAGGTTTATGTCTGTCCATATTATTGCTTTTTTGAATTACCTTCTAAACAAAATACTCAT\n-CCTTACAAACCTGCTTCCTCTTCTATGGATCCCACCACTCCATGCCCCGAAAAAAAAGAA\n-AGAAAAAGATAAGTTTTTCATAGTCACTTTAGATTATCATTTATTAAATTCTGTCGGCTC\n-AACTGATAGGAACAGTGAAATGGACTTTTCAATCATAAAAAGATAATAGAAGTTATTAAA\n-TGATTCCCTTCAAGATTATGAGCTTTTAAACTTACATATCATGCAACTATTGGGGAATTA\n-AGGGACTGGGGATTTGATGATAAATTCCAGCACCATTTTTGGTGCTTTTGTGTTTTTGCA\n-AGGTAGTTTGTTAGTGGCACATGGAAGGAGGTGCCTCATCCAATGAAATTATTAATCTTA\n-TCAACAAGAAGAAAGTCAAAACACCAAACTGTAAAAAATCCAAAAATAGCATTTTGCATT\n-GTGTACTAACTGAACAACGTACTTGCTTGACATGGTCAACTCTGGCAACCTGCGCAGTCC\n-GGGGATCAAGATACTCATCCTTATGAACCTCACTAAATGATGTAATCAGTACCTACAAAT\n-TAGTGAACAGCAACTTTACACAGCTAGATCATGAAAAATAGCTTCCAAGTGTCCATTACT\n-ACATAAATGAAAAGCATTATACTTTCTTTTTAGAAGAGGGGAACAAAATCTTAGACTTCA\n-TAAGGAACAGTTCTCCGGAAAGTTTTCTTTTCTATATTGAAGAAGTAATCATTTATTGAA\n-GTGGTGGAAATTCCCTAAGCTTTAAACAGATGTAGAGAACTTGTCCATAAACATGGTGCT\n-CAACAAACAACACCCAACTCATTCATATATAGTAGCGCCAGCATCCAAGTACCATGAAGT\n-ATATCTCTATCCTAAAAGCTTTACTTGAAGACTTATTAGATTAATCTTACTTATTTCTCA\n-TGCAACTTTTTTTTTGAAAAGTTTCTCAAGCATAACTTTTATCCTTTGTTTTCATTCAGT\n-CTTTGAGCTCTAAAGGATGCCTAGAGAGGTCATGAACCAAGTAAGGAAATTGCAACATCA\n-TATTGCTTCCAATTTACCTCATTTTTTATCTTCAACTACCGAAAACTACCAAATCTGAAA\n-TTATCAACTAAGGAAAATTACAACATCAGTACAATAAGTATTGCTTACAGTTCACTTAAT\n-ATTTCAATCTTCGACTACGGAAAACTGTCAAATCTGAAATTATCAATTTGAATGACACGA\n-TTAGTCTAACTTACATTTTCAAAGATCTAACTTACCCAATGAAAAAAGAAAACAAGAGAG\n-AGACTTACATCGCCACTTCTGTTTGGGAATTCGAGACAAATCAAGTGAGATTTGTTGTAC\n-GAAGGAAATGACTCCTCGGCCGCTTTCTTATATATATTTTCGTCCTTTAAAATAGCTCTA\n-ACATCTGCAAATCCAACCAAATGACGCTCAAAACCAAAAATGTAAAAAATAAACTGCCGA\n-TCGCAAATGAACACCAATGCGGTCACATTTTCAAGCACGAAAAAAGCTTCAAAATACAAA\n-AAACTTTAGCGCAGAAAATAAACGAAAGAGAAGAAGAAGAAGACCTTTGGCGACGTACTG\n-AATTTCGCCGGCTGGGGCATTAAGAAGGAACCATTTGGCAATCTCAAT\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/REF.fasta.fai --- a/SMART/data/REF.fasta.fai Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,198 +0,0 @@ -C10HBa0111D09_LR276 9300 48 60 61 -C11HBa0029C01_LR281 10969 9552 60 61 -C11HBa0034I10_LR282 9056 20752 60 61 -C11HBa0054I23_LR283 10301 30008 60 61 -C11HBa0062I24_LR284 10050 40531 60 61 -C11HBa0064J13_LR285 9385 50797 60 61 -C11HBa0072I13_LR286 9556 60387 60 61 -C11HBa0089M02_LR287 9244 70150 60 61 -C11HBa0096D22_LR288 9184 79597 60 61 -C11HBa0107K14_LR289 9115 88983 60 61 -C11HBa0139J14_LR291 10002 98299 60 61 -C11HBa0143O06_LR374 10785 108517 60 61 -C11HBa0161D01_LR292 9057 119530 60 61 -C11HBa0168B23_LR293 9826 128787 60 61 -C11HBa0190J03_LR294 10992 138826 60 61 -C11HBa0249E07_LR279 10008 150051 60 61 -C11HBa0303G16_LR296 9430 160274 60 61 -C11HBa0323E19_LR297 9657 169910 60 61 -C11SLe0053P22_LR298 9827 179777 60 61 -C11SLm0052K14_LR376 10013 189817 60 61 -C12HBa115G22_LR301 10021 200043 60 61 -C12HBa120K4_LR313 10271 210279 60 61 -C12HBa144B17_LR302 9247 220768 60 61 -C12HBa149G24_LR381 9271 230217 60 61 -C12HBa165B12_LR303 9257 239690 60 61 -C12HBa183M6_LR379 9473 249148 60 61 -C12HBa221M9_LR377 10755 258826 60 61 -C12HBa224N6_LR382 9130 269807 60 61 -C12HBa26C13_LR299 9139 279136 60 61 -C12HBa326K10_LR306 10414 288478 60 61 -C12HBa90D9_LR311 9638 299111 60 61 -C12HBa93P12_LR312 9510 308956 60 61 -C12SLe124D18_LR385 10545 318673 60 61 -C12SLeRI72J6_LR378 9337 329441 60 61 -C12SLm103K8_LR380 10118 338981 60 61 -C01HBa0003D15_LR7 10776 349315 60 61 -C01HBa0163B20_LR10 9321 360318 60 61 -C01HBa0216G16_LR11 10332 369845 60 61 -C01HBa0256E08_LR13 9024 380399 60 61 -C01HBa0329A12_LR14 9536 389621 60 61 -BAC19_LR16 9760 399355 60 61 -C02HBa0008G02_LR67 9205 409327 60 61 -C02HBa0011O23_LR68 9399 418733 60 61 -C02HBa0016A12_LR19 9822 428336 60 61 -C02HBa0027B01_LR21 9222 438369 60 61 -C02HBa0030A21_LR22 9147 447792 60 61 -C02HBa0046M08_LR23 10763 457140 60 61 -C02HBa0072A04_LR26 9766 468130 60 61 -C02HBa0075D08_LR28 10744 478107 60 61 -C02HBa0124N09_LR31 9335 489077 60 61 -C02HBa0155D20_LR36 10743 498616 60 61 -C02HBa0155E05_LR37 10417 509587 60 61 -C02HBa0164H08_LR38 10279 520227 60 61 -C02HBa0167J21_LR39 9925 530725 60 61 -C02HBa0185P07_LR40 9818 540863 60 61 -C02HBa0190N21_LR41 10835 550895 60 61 -C02HBa0190P16_LR331 10808 561960 60 61 -C02HBa0194L19_LR42 10280 572997 60 61 -C02HBa0204A09_LR332 10029 583498 60 61 -C02HBa0204D01_LR334 9746 593743 60 61 -C02HBa0214B22_LR325 9581 603699 60 61 -C02HBa0215M12_LR319 9918 613488 60 61 -C02HBa0228I09_LR329 10933 623621 60 61 -C02HBa0236E02_LR326 9822 634785 60 61 -C02HBa0284G15_LR47 9034 644820 60 61 -C02HBa0291P19_LR48 9826 654052 60 61 -C02HBa0329G05_LR52 9637 664090 60 61 -C02SLe0010H16_LR53 10744 673936 60 61 -C02SLe0018B07_LR335 9222 684910 60 61 -C02SLe0034H10_LR327 10833 694334 60 61 -C02SLe0127J16_LR59 10965 705396 60 61 -C02SLe0132D01_LR60 10524 716591 60 61 -C02SLm0057H03_LR336 9514 727339 60 61 -C02SLm0057H03_LR64 9170 737059 60 61 -C02SLm0057H03_LR65 9532 746429 60 61 -C03HBa0012D06_LR72 10645 756168 60 61 -C03HBa0030O03_LR74 10569 767039 60 61 -C03HBa0034B23_LR76 10005 777833 60 61 -C03HBa0040F22_LR77 10227 788053 60 61 -C03HBa0054O21_LR78 9044 798497 60 61 -C03HBa0076J13_LR79 10097 807740 60 61 -C03HBa0233O20_LR82 9753 818053 60 61 -C03HBa0295I12_LR83 10258 828017 60 61 -C03HBa0318C22_LR84 10004 838495 60 61 -C03HBa0323D22_LR85 9222 848713 60 61 -C04HBa127N12_LR346 10533 858137 60 61 -C04HBa132O11_LR104 10306 868894 60 61 -C04HBa164O3_LR344 9345 879419 60 61 -C04HBa190C13_LR106 10719 888968 60 61 -C04HBa198I15_LR107 10673 899914 60 61 -C04HBa219H8_LR109 10174 910812 60 61 -C04HBa239P14_LR111 10483 921204 60 61 -C04HBa255I2_LR112 10650 931908 60 61 -C04HBa27G19_LR337 9788 942782 60 61 -C04HBa2G1_LR120 9322 952778 60 61 -C04HBa331L22_LR115 10697 962304 60 61 -C04HBa35C16_LR339 9494 973226 60 61 -C04HBa36C23_LR91 10103 982925 60 61 -C04HBa50I18_LR341 10825 993244 60 61 -C04HBa58E11_LR93 9927 1004296 60 61 -C04HBa66O12_LR94 9355 1014433 60 61 -C04HBa68N5_LR343 9886 1023989 60 61 -C04HBa6E18_LR87 9265 1034086 60 61 -C04HBa6O16_LR123 10386 1043552 60 61 -C04HBa78E4_LR98 9994 1054158 60 61 -C04HBa78J4_LR99 9165 1064363 60 61 -C04HBa80D3_LR100 9781 1073726 60 61 -C04HBa8K13_LR338 9345 1083716 60 61 -C04HBa96I8_LR101 9693 1093262 60 61 -C04SLm14G22_LR116 10306 1103164 60 61 -C04SLm39E17_LR117 9105 1113688 60 61 -C05HBa0003C20_LR126 9460 1122990 60 61 -C05HBa0006N20_LR128 10108 1132657 60 61 -C05HBa0019C24_LR143 9514 1142982 60 61 -C05HBa0042B19_LR129 10674 1152703 60 61 -C05HBa0057G22_LR130 9023 1163602 60 61 -C05HBa0058L13_LR131 9215 1172824 60 61 -C05HBa0108A18_LR132 10114 1182244 60 61 -C05HBa0131D04_LR133 9279 1192574 60 61 -C05HBa0135A02_LR134 10620 1202057 60 61 -C05HBa0138J03_LR135 10910 1212905 60 61 -C05HBa0145P19_LR136 9141 1224045 60 61 -C05HBa0261K11_LR139 9058 1233387 60 61 -C06HBa0024F02_LR152 10452 1242645 60 61 -C06HBa0036J15_LR145 9458 1253320 60 61 -C06HBa0066D13_LR353 10505 1262985 60 61 -C06HBa0066I09_LR156 9957 1273713 60 61 -C06HBa0103N18_LR158 10350 1283886 60 61 -C06HBa0106K23_LR159 10895 1294458 60 61 -C06HBa0120H21_LR161 10738 1305584 60 61 -C06HBa0144J05_LR355 10850 1316549 60 61 -C06HBa0147H20_LR146 10693 1327629 60 61 -C06HBa0197N20_LR164 9418 1338549 60 61 -C06HBa0217M17_LR166 9470 1348172 60 61 -C06HBa0222J18_LR167 9282 1357848 60 61 -C06HBa0304P16_LR358 10525 1367334 60 61 -C06SLe0093P23_LR171 10431 1378084 60 61 -C06SLm0009E16_LR172 9523 1388737 60 61 -C06SLm0022H01_LR173 9212 1398467 60 61 -C06SLm0067G18_LR359 10587 1407882 60 61 -C07HBa0002D20_LR197 9796 1418694 60 61 -C07HBa0002M15_LR175 10456 1428703 60 61 -C07HBa0012N15_LR200 9921 1439382 60 61 -C07HBa0018L21_LR201 9169 1449517 60 61 -C07HBa0116M01_LR182 9010 1458887 60 61 -C07HBa0130B18_LR183 10208 1468097 60 61 -C07HBa0140O20_LR184 9640 1478524 60 61 -C07HBa0224G23_LR186 10880 1488374 60 61 -C07HBa0229H10_LR187 10802 1499484 60 61 -C07HBa0287B22_LR188 10024 1510516 60 61 -C07HBa0308M01_LR189 9216 1520756 60 61 -C07HBa0309B15_LR190 9063 1530174 60 61 -C07HBa0309F18_LR191 9664 1539437 60 61 -C07SLe0008H22_LR192 10612 1549312 60 61 -C07SLe0099J13_LR193 10794 1560150 60 61 -C07SLe0111B06_LR194 9814 1571170 60 61 -C07SLm0119A22_LR209 10081 1581197 60 61 -C07SLm0140K05_LR206 10879 1591498 60 61 -C08HBa0006A17_LR229 10049 1602608 60 61 -C08HBa0012O06_LR211 9339 1612873 60 61 -C08HBa0018C13_LR232 9075 1622416 60 61 -C08HBa0025D10_LR235 10483 1631692 60 61 -C08HBa0025I17_LR236 10269 1642401 60 61 -C08HBa0149J12_LR217 10855 1652891 60 61 -C08HBa0165B06_LR218 10825 1663976 60 61 -C08HBa0201M14_LR220 10831 1675031 60 61 -C08HBa0239G21_LR221 9322 1686090 60 61 -C08HBa0336I24_LR223 10943 1695617 60 61 -C08SLm0118A18_LR226 10481 1706792 60 61 -C09HBa0022M02_LR247 10139 1717497 60 61 -C09HBa0036O20_LR250 9692 1727852 60 61 -C09HBa0038L16_LR251 10860 1737755 60 61 -C09HBa0049F08_LR253 10353 1748845 60 61 -C09HBa0059I05_LR254 10352 1759421 60 61 -C09HBa0099F14_LR257 10809 1769995 60 61 -C09HBa0099P03_LR258 10156 1781034 60 61 -C09HBa0100J12_LR259 9064 1791408 60 61 -C09HBa0102E23_LR260 9715 1800672 60 61 -C09HBa0109D11_LR262 10625 1810598 60 61 -C09HBa0113I06_LR360 9962 1821449 60 61 -C09HBa0116C14_LR240 9470 1831625 60 61 -C09HBa0142I14_LR265 9190 1841301 60 61 -C09HBa0165P17_LR241 10794 1850694 60 61 -C09HBa0176I09_LR266 10260 1861717 60 61 -C09HBa0191P09_LR267 9629 1872195 60 61 -C09HBa0194K19_LR362 10346 1882034 60 61 -C09HBa0203J14_LR243 10369 1892602 60 61 -C09HBa0226D21_LR244 10625 1903193 60 61 -C09SLe0068C01_LR272 9113 1914044 60 61 -C09SLe0076N09_LR363 10488 1923358 60 61 -C09SLe0085A10_LR364 9300 1934069 60 61 -C09SLe0130H12_LR273 9470 1943571 60 61 -C09SLm0008K04_LR274 10746 1953248 60 61 -C09SLm0018L06_LR366 9448 1964222 60 61 -C09SLm0037I08_LR367 9433 1973876 60 61 -C09SLm0094A22_LR246 10193 1983516 60 61 -C09SLm0129J22_LR373 9064 1993927 60 61 -C09SLm0143I09_LR365 10488 2003192 60 61 |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/SR1.fasta --- a/SMART/data/SR1.fasta Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2500 +0,0 @@\n->HWI-EAS337_3:7:1:415:1217/1\n-GATGTGCAGACTTTTCACGCAGGACTACATCACTGT\n->HWI-EAS337_3:7:1:208:1489/1\n-GGAAACATATGCACATAAACGTTGAAATCATGCTTA\n->HWI-EAS337_3:7:1:278:1153/1\n-GAGAAAACCTGTAATAAATACTGAGAGAAAGTAGGG\n->HWI-EAS337_3:7:1:1178:755/1\n-GGTGAGAGTGGTTGGTTGATGGTAAAACCATTGAAT\n->HWI-EAS337_3:7:1:277:1259/1\n-GGGTGACAAAGAAAACAAAAGGGACATGGTACTTGG\n->HWI-EAS337_3:7:1:447:1231/1\n-GACTTGTGGAAGAGTTGGAATGGAAAGCTGGAGCCT\n->HWI-EAS337_3:7:1:300:1199/1\n-GTTTTTGCATATAGATCTCTTTGTAAAGATATCCAT\n->HWI-EAS337_3:7:1:247:1210/1\n-GATAGCTTTGACTATAGGACTTTTATGTATGTGTTG\n->HWI-EAS337_3:7:1:1154:1517/1\n-GAATGTTGCAGACCTTACTCCTACCTATGAAGCACA\n->HWI-EAS337_3:7:1:164:1869/1\n-GTTTGATAGGAATTTATTTCTTCTTCGACATCCACC\n->HWI-EAS337_3:7:1:415:1194/1\n-GATGGTTGACACATTAAGAACATTCTCACCGGTCTC\n->HWI-EAS337_3:7:1:645:1892/1\n-GATAGTAAGCACCCCTCACTTCCAACCCAAAGATTG\n->HWI-EAS337_3:7:1:33:1446/1\n-GTTATTCTTTCTTTCTCAAATGGATGCAGTAATGCA\n->HWI-EAS337_3:7:1:1194:1427/1\n-GAAAAATCACATTTTTTTGTTTGATAAAAACCCAGA\n->HWI-EAS337_3:7:1:624:1913/1\n-GACATCTTCAACTCCGGAGTTTTGAGTAACATTATA\n->HWI-EAS337_3:7:1:437:1202/1\n-GTACTTATGATGAAACTGAGATCAACTACCACCTCC\n->HWI-EAS337_3:7:1:1386:1787/1\n-GTTTAGCTAGTATTAAGGCTAGAAATGGATATGATG\n->HWI-EAS337_3:7:1:227:1155/1\n-GATAGCAGCAAGGTTATTGGAATCTAAGCAATCTAC\n->HWI-EAS337_3:7:1:472:1025/1\n-GAAGTGATACTCATAAAACTATTTAGAAAGTTAATT\n->HWI-EAS337_3:7:1:220:1482/1\n-GCTATATGAGAATTCAGGCCACTTGTAGTTCGATAA\n->HWI-EAS337_3:7:1:1699:1966/1\n-GATGAAGGATACTACAAAAAAAAGGGTTATTTTGTG\n->HWI-EAS337_3:7:1:547:1084/1\n-GTGGTCAGGTCCTCTTCAAGTGATACAATGTTCCCC\n->HWI-EAS337_3:7:1:464:1097/1\n-GAAATTGAAGCTAGTTATTGACAGTTTACCAAGTTA\n->HWI-EAS337_3:7:1:171:1480/1\n-GATAATACTATTAGCACATCAGCCTCTAGATGAGAC\n->HWI-EAS337_3:7:1:293:1251/1\n-GTGGTAGTGAGCTCCGTGGTGAACAAGATGACGGAA\n->HWI-EAS337_3:7:1:647:1863/1\n-GGGTTTCAGATTAGTAAGTTATAGTGAAAAAATATA\n->HWI-EAS337_3:7:1:263:1275/1\n-GCTACGTCTGCTCTAACTCCTAATATGATCCTGTAT\n->HWI-EAS337_3:7:1:1112:215/1\n-GGTGTTGATTTCACAAGGAGGAATACTCATCTAAAA\n->HWI-EAS337_3:7:1:319:1275/1\n-GTTATAGTTCTTGACAACAAAGTACAGAGGTGGTCC\n->HWI-EAS337_3:7:1:1310:1480/1\n-GTAGAGGAGGTAGGCTTGGTGGTCCCTCTATGGTAA\n->HWI-EAS337_3:7:1:1203:1470/1\n-GTGATATCTTTAACTAATTCTTCACGCATCTTTTCT\n->HWI-EAS337_3:7:1:415:1242/1\n-GACACATTATAAAATGATTAACAGACAGAAAGTACC\n->HWI-EAS337_3:7:1:1160:1471/1\n-GTAGTTGTGGAGAATGGTGCTTGCTTGGGTTGTTTA\n->HWI-EAS337_3:7:1:42:1475/1\n-GTTAAATGAGTTTAATGAATTAAATTAGTCTATATT\n->HWI-EAS337_3:7:1:155:1439/1\n-GAAGAGAAGCCAGATACTCAGTCTCATGGTGGCGAA\n->HWI-EAS337_3:7:1:1164:1447/1\n-GGAGAGGAAAGTGAAATTTAGGTTTAGACTTCGTTT\n->HWI-EAS337_3:7:1:277:1169/1\n-GGTTAAGCACAGCTGCACCAGCCAAAGCAGCAGAGC\n->HWI-EAS337_3:7:1:359:1249/1\n-GCTACATGTTTATGTGAGAAATATTATTTCAGTTGT\n->HWI-EAS337_3:7:1:1230:1425/1\n-GAATTCTGCGGCTAACTGTGGCATCGTGCAGCTGAT\n->HWI-EAS337_3:7:1:1526:1772/1\n-GGATAATTCATCATAAAATAGACCTTAGGGCAGTAG\n->HWI-EAS337_3:7:1:1171:720/1\n-GTTGATTGCGGAATAATATTTGCTTTTTTAGTTTTC\n->HWI-EAS337_3:7:1:1663:896/1\n-GTTGGGTTGGTTGAGCGAGAGGATTTTGCATCTGGT\n->HWI-EAS337_3:7:1:382:1159/1\n-GTGATAGGACCATTCCATAGTTTAGATGTATAATTG\n->HWI-EAS337_3:7:1:113:1855/1\n-GAATTTCAGCTTGCAAACTGTTTGGCTTTCCATTCA\n->HWI-EAS337_3:7:1:1356:1757/1\n-GTACTGAAAGATATGATAATATACATTGTTTGACTT\n->HWI-EAS337_3:7:1:124:757/1\n-GATACATAACACAATCAGTTGATCGAAACAAAACCA\n->HWI-EAS337_3:7:1:1211:751/1\n-GAAAGGTTAAGGCAAGGCCTGCTTAGTAAACAGGGA\n->HWI-EAS337_3:7:1:524:840/1\n-GTGTAGTTGGCTTCATATCAATTGACGGATGTTTCA\n->HWI-EAS337_3:7:1:478:1078/1\n-GTTAAGTGTGGAAATGAGAAGTTCTAATAGTACTTG\n->HWI-EAS337_3:7:1:1250:656/1\n-GAAGTTTTTTTAACGAGTGCACACGTTAGAACTCGC\n->HWI-EAS337_3:7:1:1301:1484/1\n-GTTGCGGAAGGAGCAAAGGCATTGTATGTAGTGTCA\n->HWI-EAS337_3:7:1:1036:1425/1\n-GGTTGTCAAGCGTTCAGCTCGAGATATATAATGTGA\n->HWI-EAS337_3:7:1:165:1435/1\n-GAGCAAAAGGGGTTGTGACTCTTGAAGAGCTGAAGA\n->HWI-EAS337_3:7:1:612:13/1\n-GGTAACATAGAGGAGGAAATATGGTGAAAACTTGAA\n->HWI-EAS337_3:7:1:485:1045/1\n-GTAACTTTATTTTATAATTTTTGATTTTTATCCGAA\n->HWI-EAS337_3:7:1:609:1117/1\n-GCAATTACAATAACAGGAAATACATCTAGCAGACTT\n->HWI-EAS337_3:7:1:1182:1510/1\n-GGGAACCTAAAAGGCAAAATGAATTGAGTCTGTATT\n->HWI-EAS337_3:7:1:1530:1678/1\n-GTTTTCAAACACAAACTACTTCTCCTAAAGCGGAAG\n->HWI-EAS337_3:7:1:1745:324'..b'>HWI-EAS337_3:7:1:1190:1457/1\n-GGAGCTAAAGTCCTAAGCTTGAGATCCAATAAACTG\n->HWI-EAS337_3:7:1:1067:1958/1\n-GTTCATGACATCCACCAACTTGTTTGTCTGTGGCTC\n->HWI-EAS337_3:7:1:87:714/1\n-GTGAGGAAAATGAAAAGTAAATAGGCAGATGCAGTA\n->HWI-EAS337_3:7:1:566:576/1\n-GAACACAGGGCTTCAGGGTCTAATATCCTGGCAGCG\n->HWI-EAS337_3:7:1:1316:1455/1\n-GAATTTATTTCAGTTCTTCTATTCTTTTTCTCTTCA\n->HWI-EAS337_3:7:1:1734:1346/1\n-GACACCTGACAGGAAGGGATCAACGAGCTATCTTTA\n->HWI-EAS337_3:7:1:1315:1665/1\n-GATCTTCTGAACGTTGAAACTTTAATAGTTCGAGGA\n->HWI-EAS337_3:7:1:319:1450/1\n-GTCCCCCATAATGTTCTTGATAACCTTCCTCTTTCC\n->HWI-EAS337_3:7:1:1565:1478/1\n-GATCCTAACTTGCTTGGAACTGAGATATAGTTGTTG\n->HWI-EAS337_3:7:1:33:25/1\n-GAATATAATCTTAAACATGTAGAGTTTTGAATACTT\n->HWI-EAS337_3:7:1:1281:1649/1\n-GATTAATTCCGTTAGTGAAAAATACAAAATGGAATT\n->HWI-EAS337_3:7:1:783:509/1\n-GTCATAGTTTTAAGGCGTGGAAACAGCCTCTAGCAG\n->HWI-EAS337_3:7:1:527:1823/1\n-GTCGGGACCGGAGAAAAGTATTATTTTAGAGATTAT\n->HWI-EAS337_3:7:1:361:602/1\n-GAAGCGAAAGGGCCATGTTCTTCGTACCTCCGTACA\n->HWI-EAS337_3:7:1:1111:669/1\n-GTGTAGTCATGTGAGGCTTTTGTCTCAGAAAAAAGT\n->HWI-EAS337_3:7:1:1404:1238/1\n-GTAAATTAGGTATAGAAGGAGTAGAGAACAATCTTT\n->HWI-EAS337_3:7:1:1325:1626/1\n-GTATGCCAGAGCGTCTTTTTCCTTTGGCATGGGGGC\n->HWI-EAS337_3:7:1:625:642/1\n-GAAACTGTAGCTATATGACTATCATTTGAATTTTGT\n->HWI-EAS337_3:7:1:1377:1833/1\n-GAAAATGCACCTAAAGTTCTCCCTAAAAACTACTCG\n->HWI-EAS337_3:7:1:964:815/1\n-GAACCCTACGGATGGAAGAGGAAAGGCGAGGATTAA\n->HWI-EAS337_3:7:1:283:1284/1\n-GTATGAAAAGCTTCCACATCCCCACTGGATGTTGAC\n->HWI-EAS337_3:7:1:374:1453/1\n-GTCAGTCTATGAGCGAATCAGAATGATATTATTGGA\n->HWI-EAS337_3:7:1:98:638/1\n-GTTACGTTTTCGTATTTGAATGATGTGATCTCAGGG\n->HWI-EAS337_3:7:1:309:1564/1\n-GTCTGATAATTTTTCCTGTTTTCTATTTATGTACCA\n->HWI-EAS337_3:7:1:863:418/1\n-GATAAAACATAAAAGAAATTCCTTCTATAATGAGCA\n->HWI-EAS337_3:7:1:1532:1997/1\n-GTTGTATTTCTAAATGTTTCTACTCCGATTTTTTTT\n->HWI-EAS337_3:7:1:1079:566/1\n-GAGTAACGTTTATGGAATCTACATAATTCATTATTA\n->HWI-EAS337_3:7:1:42:911/1\n-GAGAAAACCATTCACCATCTTTTGCCGTTATAGTGC\n->HWI-EAS337_3:7:1:428:1520/1\n-GCAAAGAAAGAAGGATTTCCTAACCAAGAAGATTTT\n->HWI-EAS337_3:7:1:986:591/1\n-GAGTTTCTTGCTCCACCACCTTTACCGAAATCTCCA\n->HWI-EAS337_3:7:1:181:1099/1\n-GGTCGACGTAAGAGATCTGCAGGGCTATTACTCATT\n->HWI-EAS337_3:7:1:509:832/1\n-GTGAAGTATGGGTGGAAATGCTTGCGTATGCTGCTA\n->HWI-EAS337_3:7:1:510:597/1\n-GGGTCTGGAATAGTAATGCGCTGATTCTAGTAAAGT\n->HWI-EAS337_3:7:1:1765:1489/1\n-GTCAATTTTTTCTTTGTTTAAATCCGGGGAGGCTAG\n->HWI-EAS337_3:7:1:417:1560/1\n-GTAACCTTCCCAGTGTCTCCTTAAGAAAGACTTGGA\n->HWI-EAS337_3:7:1:1047:854/1\n-GTTGAAATTCCTGATTTTCCATGTGCATCATAAGCC\n->HWI-EAS337_3:7:1:1296:202/1\n-GGTGTTGGAGTTGGATTTGTTTCTGCTTTGATATCC\n->HWI-EAS337_3:7:1:502:642/1\n-GATGATTCTTGCTGGTTAAGTTGAGATGGGTTATAA\n->HWI-EAS337_3:7:1:82:1651/1\n-GGCATCCTGTTCATCCTTCTCTTCATTTTTAGGCGT\n->HWI-EAS337_3:7:1:1505:1274/1\n-GAAACTTTTCAAAAAAAAAGTTGCATGAGAAATAAG\n->HWI-EAS337_3:7:1:5:1770/1\n-GTGTGAAAAAGTATTTCATTCACATATTGAGTTGTT\n->HWI-EAS337_3:7:1:115:1005/1\n-GATTTTACTGGAATGGGGAAGGGTGAGGCATGGGTG\n->HWI-EAS337_3:7:1:354:1708/1\n-GCATCCGACAGTGACTTAGACGATGAGGAATACGAG\n->HWI-EAS337_3:7:1:1639:1500/1\n-GTGATTATTATCTAACTCTGCAACAGCATCCAGGGA\n->HWI-EAS337_3:7:1:766:243/1\n-GTGGCATCTATGGAAGATAAATTGGAGATTGTTGCT\n->HWI-EAS337_3:7:1:920:144/1\n-GTGCGATCACACTGTTTATGTTGTTGTTGATCATTG\n->HWI-EAS337_3:7:1:389:268/1\n-GGTCAATTAGAGAGGGCAACCACCCTCAAAGAATTT\n->HWI-EAS337_3:7:1:294:1868/1\n-GAAAAAAAATTGTTTGTCTTGAATTAATGTTTCAAT\n->HWI-EAS337_3:7:1:1147:62/1\n-GAATTCCCCTCAGGTTGGAGTTGTGCACTTGGCACT\n->HWI-EAS337_3:7:1:787:1759/1\n-GGTTTTATTAGAATTGGTAGCTGTTCTGATTTTCTG\n->HWI-EAS337_3:7:1:425:1939/1\n-GCTAATTGTGGTGTCTGGGTCTATGTGGCTAAACTT\n->HWI-EAS337_3:7:1:187:1132/1\n-GTGGGAGAGGCAAGGGGCTTGGCTCATATCCTCTTC\n->HWI-EAS337_3:7:1:1739:1840/1\n-GGAGGGGTGAAATCGTTTCTGAAAAATAATGAAATG\n->HWI-EAS337_3:7:1:1505:1876/1\n-GAAAGATCAAGTGTTGTCAAGTTCACTAGTTTAGAG\n->HWI-EAS337_3:7:1:447:192/1\n-GACTATGCCTAGCAGCTGAAATCACCACAACAAGTT\n->HWI-EAS337_3:7:1:21:2019/1\n-GTATGAGGTAAAAGATGATAACCTGTCTTCCAGCCC\n->HWI-EAS337_3:7:1:1593:652/1\n-GTGATGAGTAAAACATCATCATATGAACTTGAAGAG\n->HWI-EAS337_3:7:1:1254:1660/1\n-GAAGTTTGTAATTCCTTTTAGGATTGTGGTTAACAT\n->HWI-EAS337_3:7:1:291:629/1\n-GTAGAGGAGGTAGGCTTGGTGGTCCCTCTATGGTAA\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/SR1.fastq --- a/SMART/data/SR1.fastq Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5000 +0,0 @@\n-@HWI-EAS337_3:7:1:415:1217/1\n-GATGTGCAGACTTTTCACGCAGGACTACATCACTGT\n-+HWI-EAS337_3:7:1:415:1217/1\n-WWWVVVWPWWWVWWWWVVVVKVPWWVVWVWUUQUTQ\n-@HWI-EAS337_3:7:1:208:1489/1\n-GGAAACATATGCACATAAACGTTGAAATCATGCTTA\n-+HWI-EAS337_3:7:1:208:1489/1\n-WWWWWWWWWWWWWWWWWVWWVWWVWWWWWWUUUUUU\n-@HWI-EAS337_3:7:1:278:1153/1\n-GAGAAAACCTGTAATAAATACTGAGAGAAAGTAGGG\n-+HWI-EAS337_3:7:1:278:1153/1\n-WWWWWWWWWWWWWWWWWWWWWWVWVVVWWVUUUUUR\n-@HWI-EAS337_3:7:1:1178:755/1\n-GGTGAGAGTGGTTGGTTGATGGTAAAACCATTGAAT\n-+HWI-EAS337_3:7:1:1178:755/1\n-WWWWWWWWWVWWWVVWWVVWVVVVWVWVVVUUUUUU\n-@HWI-EAS337_3:7:1:277:1259/1\n-GGGTGACAAAGAAAACAAAAGGGACATGGTACTTGG\n-+HWI-EAS337_3:7:1:277:1259/1\n-WWWWWWWWWWWWWWWWWWWWWWVWWWWWWVUUUUUU\n-@HWI-EAS337_3:7:1:447:1231/1\n-GACTTGTGGAAGAGTTGGAATGGAAAGCTGGAGCCT\n-+HWI-EAS337_3:7:1:447:1231/1\n-WWWWWWWWWWWVWVWWWVWWWVVVVVVVVVURUSUU\n-@HWI-EAS337_3:7:1:300:1199/1\n-GTTTTTGCATATAGATCTCTTTGTAAAGATATCCAT\n-+HWI-EAS337_3:7:1:300:1199/1\n-WVWWWWWWWWWWWVWWWWWWWWQWVVVTWWUUUURU\n-@HWI-EAS337_3:7:1:247:1210/1\n-GATAGCTTTGACTATAGGACTTTTATGTATGTGTTG\n-+HWI-EAS337_3:7:1:247:1210/1\n-WWWWWWWWWWWWVWWWVVWWWWWWWWTVVWRULUUR\n-@HWI-EAS337_3:7:1:1154:1517/1\n-GAATGTTGCAGACCTTACTCCTACCTATGAAGCACA\n-+HWI-EAS337_3:7:1:1154:1517/1\n-WWWWWWWVWWVWWWWWWWWWWWWWVWVWVWUSUUUU\n-@HWI-EAS337_3:7:1:164:1869/1\n-GTTTGATAGGAATTTATTTCTTCTTCGACATCCACC\n-+HWI-EAS337_3:7:1:164:1869/1\n-WWWWWWWWVVWWWWWWWWWWWWWWWWQWWWUUUUUU\n-@HWI-EAS337_3:7:1:415:1194/1\n-GATGGTTGACACATTAAGAACATTCTCACCGGTCTC\n-+HWI-EAS337_3:7:1:415:1194/1\n-WWWWWWWWWWWWWWWWWVWVWVWWWWWWWVSUUUUU\n-@HWI-EAS337_3:7:1:645:1892/1\n-GATAGTAAGCACCCCTCACTTCCAACCCAAAGATTG\n-+HWI-EAS337_3:7:1:645:1892/1\n-WWWWWWWWWWWWWWWWWVWWWWWVVWVWWVUUUUUU\n-@HWI-EAS337_3:7:1:33:1446/1\n-GTTATTCTTTCTTTCTCAAATGGATGCAGTAATGCA\n-+HWI-EAS337_3:7:1:33:1446/1\n-WWWWWWWWWWWWWWWWWWWWWUQWWVVWQWUUUSUU\n-@HWI-EAS337_3:7:1:1194:1427/1\n-GAAAAATCACATTTTTTTGTTTGATAAAAACCCAGA\n-+HWI-EAS337_3:7:1:1194:1427/1\n-WWWWWWWWVWVWWWWWWWVWWWUWWWWWWWUUUUSU\n-@HWI-EAS337_3:7:1:624:1913/1\n-GACATCTTCAACTCCGGAGTTTTGAGTAACATTATA\n-+HWI-EAS337_3:7:1:624:1913/1\n-WWWWWWWWWWVWWWWVVVVWWWWVVVWWVWUUUUUU\n-@HWI-EAS337_3:7:1:437:1202/1\n-GTACTTATGATGAAACTGAGATCAACTACCACCTCC\n-+HWI-EAS337_3:7:1:437:1202/1\n-WWWWWVWWWVWVWWWWWWWWVWWWWVWVVVUUUUUU\n-@HWI-EAS337_3:7:1:1386:1787/1\n-GTTTAGCTAGTATTAAGGCTAGAAATGGATATGATG\n-+HWI-EAS337_3:7:1:1386:1787/1\n-WWWWWWWWWWWWWWWWVVWWWVWVVWVVVWUUSUUO\n-@HWI-EAS337_3:7:1:227:1155/1\n-GATAGCAGCAAGGTTATTGGAATCTAAGCAATCTAC\n-+HWI-EAS337_3:7:1:227:1155/1\n-WWVWWVWWVVWVVIWVWVVUWVVVVWVTVVUUUUSU\n-@HWI-EAS337_3:7:1:472:1025/1\n-GAAGTGATACTCATAAAACTATTTAGAAAGTTAATT\n-+HWI-EAS337_3:7:1:472:1025/1\n-WWWWWWWWWWWWWWWVWVWWWWWWVVWWWVUUUUUU\n-@HWI-EAS337_3:7:1:220:1482/1\n-GCTATATGAGAATTCAGGCCACTTGTAGTTCGATAA\n-+HWI-EAS337_3:7:1:220:1482/1\n-WWWWWWWWWVWWWWWWWVWWWWWWWWVVWWURUUUU\n-@HWI-EAS337_3:7:1:1699:1966/1\n-GATGAAGGATACTACAAAAAAAAGGGTTATTTTGTG\n-+HWI-EAS337_3:7:1:1699:1966/1\n-WWWWWWWWWWWWWWWWVWVWWWWWWWVWWWUUUSUR\n-@HWI-EAS337_3:7:1:547:1084/1\n-GTGGTCAGGTCCTCTTCAAGTGATACAATGTTCCCC\n-+HWI-EAS337_3:7:1:547:1084/1\n-WWWWWWWWWWWWWWWWWWVVWVWWWWWWWVUUUUSU\n-@HWI-EAS337_3:7:1:464:1097/1\n-GAAATTGAAGCTAGTTATTGACAGTTTACCAAGTTA\n-+HWI-EAS337_3:7:1:464:1097/1\n-WWWWWWWWWWWVWWVWWWWWWWWVVWWWWVUUUUUR\n-@HWI-EAS337_3:7:1:171:1480/1\n-GATAATACTATTAGCACATCAGCCTCTAGATGAGAC\n-+HWI-EAS337_3:7:1:171:1480/1\n-WWWWWWWWWWWWWVWWWWWWWVWWWWWWTVUUUUUU\n-@HWI-EAS337_3:7:1:293:1251/1\n-GTGGTAGTGAGCTCCGTGGTGAACAAGATGACGGAA\n-+HWI-EAS337_3:7:1:293:1251/1\n-WWWWWWWVWVWWWWVVWWVVVVVVWVVVVVRPUURR\n-@HWI-EAS337_3:7:1:647:1863/1\n-GGGTTTCAGATTAGTAAGTTATAGTGAAAAAATATA\n-+HWI-EAS337_3:7:1:647:1863/1\n-WWVWWWWWVWWWWVWWVVWWWWWWWVWVVWUUUUUU\n-@HWI-EAS337_3:7:1:263:1275/1\n-GCTACGTCTGCTCTAACTCCTAATATGATCCTGTAT\n-+HWI-EAS337_3:7:1:263:1275/1\n-WWWWWWWWWWWWWWWWWWWWWVWWWWQVWWUUOUUU\n-@HWI-EAS337_3:7:1:1112:215/1\n-GGTGTTGATTTCACAAGGAGGAATACTCATCTAAAA\n-+HWI-EAS337_3:7:1:1112:215/1\n-WWVWWVVWVVWWWVWWVUWVVVWWWVWTVWUUUUUU\n-@HWI-EAS337_3:7:1:319:1275/1\n-GTTATAGTTCTTGACAACAAAGTACAGAGGTGGTCC\n-+HWI-EAS337_3:7:1:319:1275/1\n-WWWWWWWWWWWWVWWWWWWWWWWWWWVWVWUUSUUU\n-@HWI-EAS337_3:7:1:1310:1480/1'..b'A\n-+HWI-EAS337_3:7:1:986:591/1\n-WWWWWWWWWVWWWWWWWWWWWWWVWVVWVVUUUUUR\n-@HWI-EAS337_3:7:1:181:1099/1\n-GGTCGACGTAAGAGATCTGCAGGGCTATTACTCATT\n-+HWI-EAS337_3:7:1:181:1099/1\n-WWWWWWWWWWWWWVWWWWWWWVVWWWVWWVUUUUUU\n-@HWI-EAS337_3:7:1:509:832/1\n-GTGAAGTATGGGTGGAAATGCTTGCGTATGCTGCTA\n-+HWI-EAS337_3:7:1:509:832/1\n-WWWWVWWWWVVWWWWWWVWVWWWVVVVVWVSUUUUR\n-@HWI-EAS337_3:7:1:510:597/1\n-GGGTCTGGAATAGTAATGCGCTGATTCTAGTAAAGT\n-+HWI-EAS337_3:7:1:510:597/1\n-VWWWVWWWWWWWWWWWWVWWWWWVWWWWVVUUUUUU\n-@HWI-EAS337_3:7:1:1765:1489/1\n-GTCAATTTTTTCTTTGTTTAAATCCGGGGAGGCTAG\n-+HWI-EAS337_3:7:1:1765:1489/1\n-WVWWVWWWWWWWWWWVWWWWWWWWWQQVTVUSUUUR\n-@HWI-EAS337_3:7:1:417:1560/1\n-GTAACCTTCCCAGTGTCTCCTTAAGAAAGACTTGGA\n-+HWI-EAS337_3:7:1:417:1560/1\n-WWWWVWWSWSVWVVVVWWWWWWWWVSWWWWUQUUQU\n-@HWI-EAS337_3:7:1:1047:854/1\n-GTTGAAATTCCTGATTTTCCATGTGCATCATAAGCC\n-+HWI-EAS337_3:7:1:1047:854/1\n-WWWWWVWWWWWWWWUWWWWWVWVWVVVWVVUUUUUU\n-@HWI-EAS337_3:7:1:1296:202/1\n-GGTGTTGGAGTTGGATTTGTTTCTGCTTTGATATCC\n-+HWI-EAS337_3:7:1:1296:202/1\n-WWWWWWWVWVWWWVVWWWWWWWWWVVWWWTUUUUUF\n-@HWI-EAS337_3:7:1:502:642/1\n-GATGATTCTTGCTGGTTAAGTTGAGATGGGTTATAA\n-+HWI-EAS337_3:7:1:502:642/1\n-WWWWWVPVVVWWWVVVWWWVWWSVVVWVVVUUUUUR\n-@HWI-EAS337_3:7:1:82:1651/1\n-GGCATCCTGTTCATCCTTCTCTTCATTTTTAGGCGT\n-+HWI-EAS337_3:7:1:82:1651/1\n-WWWWWWWWVWWWWWWWWVWWWWWWVWWWWWUKJUQU\n-@HWI-EAS337_3:7:1:1505:1274/1\n-GAAACTTTTCAAAAAAAAAGTTGCATGAGAAATAAG\n-+HWI-EAS337_3:7:1:1505:1274/1\n-WWWWWWWWWWWWVWWWWWWWVWWWWWWVWWSUUUUR\n-@HWI-EAS337_3:7:1:5:1770/1\n-GTGTGAAAAAGTATTTCATTCACATATTGAGTTGTT\n-+HWI-EAS337_3:7:1:5:1770/1\n-WWWWWWWWWWVWWWWWWWWWWWWWWWWWVVSUUQUU\n-@HWI-EAS337_3:7:1:115:1005/1\n-GATTTTACTGGAATGGGGAAGGGTGAGGCATGGGTG\n-+HWI-EAS337_3:7:1:115:1005/1\n-WWWWWWWWWVVWWWVVVVWWVVVWWWVVWVUUUUUU\n-@HWI-EAS337_3:7:1:354:1708/1\n-GCATCCGACAGTGACTTAGACGATGAGGAATACGAG\n-+HWI-EAS337_3:7:1:354:1708/1\n-WWWWWWWWWWWWVWWWWWVWWVWWVWWVWWUUUUUR\n-@HWI-EAS337_3:7:1:1639:1500/1\n-GTGATTATTATCTAACTCTGCAACAGCATCCAGGGA\n-+HWI-EAS337_3:7:1:1639:1500/1\n-WWWWWWVVWWWWWVVWVVWUVVVVVVVVWVUUUUUR\n-@HWI-EAS337_3:7:1:766:243/1\n-GTGGCATCTATGGAAGATAAATTGGAGATTGTTGCT\n-+HWI-EAS337_3:7:1:766:243/1\n-WWVWWWWWWWWVVWWVWWWWWWWVVVTVWWRUUJSU\n-@HWI-EAS337_3:7:1:920:144/1\n-GTGCGATCACACTGTTTATGTTGTTGTTGATCATTG\n-+HWI-EAS337_3:7:1:920:144/1\n-WWVVWWWWWVWPWVWWVWWSWVSWWHWWLVUCPUUH\n-@HWI-EAS337_3:7:1:389:268/1\n-GGTCAATTAGAGAGGGCAACCACCCTCAAAGAATTT\n-+HWI-EAS337_3:7:1:389:268/1\n-WWWWWWWWWVWWWWVVWWWWWWWWWWWWVVSUUUUU\n-@HWI-EAS337_3:7:1:294:1868/1\n-GAAAAAAAATTGTTTGTCTTGAATTAATGTTTCAAT\n-+HWI-EAS337_3:7:1:294:1868/1\n-VWVWWWWWWWWVQWWWWOWVVWWVWVVWQWUURULU\n-@HWI-EAS337_3:7:1:1147:62/1\n-GAATTCCCCTCAGGTTGGAGTTGTGCACTTGGCACT\n-+HWI-EAS337_3:7:1:1147:62/1\n-WWWWWWWWWWWWVWWWWWWVWWVWVVWVVWUUUUUU\n-@HWI-EAS337_3:7:1:787:1759/1\n-GGTTTTATTAGAATTGGTAGCTGTTCTGATTTTCTG\n-+HWI-EAS337_3:7:1:787:1759/1\n-WVVWWWWVWWWWWWWVUWWUWWUVWVVTVVUUUUUH\n-@HWI-EAS337_3:7:1:425:1939/1\n-GCTAATTGTGGTGTCTGGGTCTATGTGGCTAAACTT\n-+HWI-EAS337_3:7:1:425:1939/1\n-WWWWVWWVWWWWVWWWVVVVWWWVVWVVVWUUUUUU\n-@HWI-EAS337_3:7:1:187:1132/1\n-GTGGGAGAGGCAAGGGGCTTGGCTCATATCCTCTTC\n-+HWI-EAS337_3:7:1:187:1132/1\n-WVWWWWWWWWWWWWWWWWWWWTVWVWWWVVUUUUUU\n-@HWI-EAS337_3:7:1:1739:1840/1\n-GGAGGGGTGAAATCGTTTCTGAAAAATAATGAAATG\n-+HWI-EAS337_3:7:1:1739:1840/1\n-WWVWWWWWWWWWWWWWWVTWWWVVVWWWWWUUUUUU\n-@HWI-EAS337_3:7:1:1505:1876/1\n-GAAAGATCAAGTGTTGTCAAGTTCACTAGTTTAGAG\n-+HWI-EAS337_3:7:1:1505:1876/1\n-WWWWWWWWWWWWWWWWWWWWVWWVWWWVVVUUUSUR\n-@HWI-EAS337_3:7:1:447:192/1\n-GACTATGCCTAGCAGCTGAAATCACCACAACAAGTT\n-+HWI-EAS337_3:7:1:447:192/1\n-WWWWWWWWWWWWWWWTWWWVVWWVWWWWWVUUUUUU\n-@HWI-EAS337_3:7:1:21:2019/1\n-GTATGAGGTAAAAGATGATAACCTGTCTTCCAGCCC\n-+HWI-EAS337_3:7:1:21:2019/1\n-VWWVVWWVVWWWWWWWWWWWWWWWQVVWWWUURUUU\n-@HWI-EAS337_3:7:1:1593:652/1\n-GTGATGAGTAAAACATCATCATATGAACTTGAAGAG\n-+HWI-EAS337_3:7:1:1593:652/1\n-WWWVWVWWVWVWWVWWWWWWVVWWVWWVWWUUUSUU\n-@HWI-EAS337_3:7:1:1254:1660/1\n-GAAGTTTGTAATTCCTTTTAGGATTGTGGTTAACAT\n-+HWI-EAS337_3:7:1:1254:1660/1\n-WWWVVWWWWWWWWWWWVWVWVUWWWTWVQWUUUUMU\n-@HWI-EAS337_3:7:1:291:629/1\n-GTAGAGGAGGTAGGCTTGGTGGTCCCTCTATGGTAA\n-+HWI-EAS337_3:7:1:291:629/1\n-WWWWWWWWWWVVVWVWVVWTWWKOVVTRVSUSSMFR\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/SR2.fastq --- a/SMART/data/SR2.fastq Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5000 +0,0 @@\n-@HWI-EAS337_3:7:1:415:1217/2\n-TAAGAACTTGGCTGATCGCCTACTTACTGCTTTTAC\n-+HWI-EAS337_3:7:1:415:1217/2\n-VWWWVWVVVVVVVVUVWVWVVWWVWVVVUVTTTTTN\n-@HWI-EAS337_3:7:1:208:1489/2\n-CGTGTTTTTGGTTGTGCATAAGGCTTTTTAAAGTAA\n-+HWI-EAS337_3:7:1:208:1489/2\n-WWWWWWWWWVVWWQWVWVWWVUVWWWWWWVRTRTTR\n-@HWI-EAS337_3:7:1:278:1153/2\n-GTCAGGCCGCATTGATGGGGGATGGGTTTCCCCCCA\n-+HWI-EAS337_3:7:1:278:1153/2\n-WWWVWWWWWWWWWVVVVVVVVVVWWWVVVVTTTTTR\n-@HWI-EAS337_3:7:1:1178:755/2\n-GACATTTCAATTACATTCATCTTACCATCACCTATA\n-+HWI-EAS337_3:7:1:1178:755/2\n-WVWVWWWWWVWWVWWVWWVVWWWVVWVWVVTTTTTR\n-@HWI-EAS337_3:7:1:277:1259/2\n-TTTTGGCTCATCAGGATCTTCTGAATCACTTGAAGA\n-+HWI-EAS337_3:7:1:277:1259/2\n-WWWWWWWWWWWWWWVVWWWWWVVVVWWVWWTRTTTS\n-@HWI-EAS337_3:7:1:447:1231/2\n-TCAACAAGAGAAAGGAGACGAAAAAGTAAATCCAAC\n-+HWI-EAS337_3:7:1:447:1231/2\n-WWWWWWWWVWWWWVVWWWWWVVWWWWVVWWTTTTTR\n-@HWI-EAS337_3:7:1:300:1199/2\n-AAAGGTATTGGTTATGCTGAAATGTTTTCTCCTATT\n-+HWI-EAS337_3:7:1:300:1199/2\n-WWWWVVWWWWVVVVWVVWVWWVWVWWWWVWTTTTTS\n-@HWI-EAS337_3:7:1:247:1210/2\n-AGCTATTACCAAAATTAAACTTCACTGCTCAAAACG\n-+HWI-EAS337_3:7:1:247:1210/2\n-VWWVWWWWWWWVWVKWWVVWWWVWWVVWVWTTTTTR\n-@HWI-EAS337_3:7:1:1154:1517/2\n-CTAACTTCAATAATCAAGCTTGTCAGTGGAAGAAAA\n-+HWI-EAS337_3:7:1:1154:1517/2\n-WWWWWWWWVVWVVWWVVVWWWVWVVVVVVVTTTTTR\n-@HWI-EAS337_3:7:1:164:1869/2\n-TAATGTCCTAGAGAAGAAGTCCTTGTGGTGGATGTC\n-+HWI-EAS337_3:7:1:164:1869/2\n-WWWWVWWWWWVWVWWWWWVWWWWWVWWVVVTTTTTN\n-@HWI-EAS337_3:7:1:415:1194/2\n-GAGATGTATTCAAGCTAAGCTTCAAGCAGCGCAGAG\n-+HWI-EAS337_3:7:1:415:1194/2\n-WWWWWWWWWWWWWVWWWVWWWWWVVVVVVWTTTTTR\n-@HWI-EAS337_3:7:1:645:1892/2\n-TTATTGTGGAGGTACAAAAAAGATATCTGCAACTAT\n-+HWI-EAS337_3:7:1:645:1892/2\n-WWWWWVWVVWVVVWVVWVVVVVVWVWWWVWTTTTTR\n-@HWI-EAS337_3:7:1:33:1446/2\n-TTTTGGAATAAAATGATATCTGCATCTGTTGAATCT\n-+HWI-EAS337_3:7:1:33:1446/2\n-WWWWWVWWWWWVWWVWWWWWWVWWWWWVWWTTTTTS\n-@HWI-EAS337_3:7:1:1194:1427/2\n-TGTAAAAAGCTTTGTTCAGCTGTGACAAGAAGAGAA\n-+HWI-EAS337_3:7:1:1194:1427/2\n-WWWWWWVVWWWWWWVWWVVWWVWUVVVVWVTTTTTR\n-@HWI-EAS337_3:7:1:624:1913/2\n-CAATATGCAGTTGTCAAGTAAGGGAAGTTCACCATT\n-+HWI-EAS337_3:7:1:624:1913/2\n-WWWWVWVWVVWWVVWVWVWVVUVUVVVWWVTTTTTR\n-@HWI-EAS337_3:7:1:437:1202/2\n-GACTGAGATATTAATTAAGGAGATAGATATCTCTAG\n-+HWI-EAS337_3:7:1:437:1202/2\n-WWWWWVWVWVWWVWWVWVVWWVWVWVWWWVTTTTTR\n-@HWI-EAS337_3:7:1:1386:1787/2\n-AACTAAACACTTACCAAAATCACCTTGTTTAGCAGC\n-+HWI-EAS337_3:7:1:1386:1787/2\n-WWWWWWWWVWVWVWWQVVVVVWWWWVVWVWTRTTTR\n-@HWI-EAS337_3:7:1:227:1155/2\n-ACTAAGAACTTGAGAATTGACAGAACCTGTGGACAA\n-+HWI-EAS337_3:7:1:227:1155/2\n-WWVVWWVVWWVVWVWWWVVVWVVVVVVVVVTTTTTP\n-@HWI-EAS337_3:7:1:472:1025/2\n-TTCTACTTAATTTTATTCAATGATATTTAATTAAAA\n-+HWI-EAS337_3:7:1:472:1025/2\n-WWWWWWWWWVWWWWWWWWWVWVWWVWWWVWTTTTTS\n-@HWI-EAS337_3:7:1:220:1482/2\n-GATTCAATGTTGAAAACTCGGCTGTATTCCAACATT\n-+HWI-EAS337_3:7:1:220:1482/2\n-WWWWWWWWVWWVWWWVWWWVVWWVVOVWUVOTROTR\n-@HWI-EAS337_3:7:1:1699:1966/2\n-ATTTTGTGTGGATCAAAAACTCCCACAGATCGATAT\n-+HWI-EAS337_3:7:1:1699:1966/2\n-VWWWWVVVWVVVWWVWVVVWWWVVVVVVVVTTTTTS\n-@HWI-EAS337_3:7:1:547:1084/2\n-ATTTTCAGATTCTTTCAAATAAGGTTCACTCGTTAG\n-+HWI-EAS337_3:7:1:547:1084/2\n-VWWWWWWVWWWWWWWWVWVWVVUVWWWVVWTTTTTN\n-@HWI-EAS337_3:7:1:464:1097/2\n-TCTACTCTCCTTACTCGGTTTGTTGGATTTCATTGG\n-+HWI-EAS337_3:7:1:464:1097/2\n-VWVVWWWWVWVWVWVWVVUWVVWWVUVWWWTQTTCN\n-@HWI-EAS337_3:7:1:171:1480/2\n-AGATCATATCCTACCCTACTGTGGCAAAGGCGTGCT\n-+HWI-EAS337_3:7:1:171:1480/2\n-VWWWWWWWWWWWVWWWVWWVVVVVWWVVVVTTTTTS\n-@HWI-EAS337_3:7:1:293:1251/2\n-CATATGTCCCAATGAAGAGGAGATGTGCATATGTAC\n-+HWI-EAS337_3:7:1:293:1251/2\n-WWWWWWWWWWWVWWWWWWWVVWWVWVVVVVTTTTTR\n-@HWI-EAS337_3:7:1:647:1863/2\n-TTGAAATGAAAAGAGAATGTACTGCAAACGATCTTC\n-+HWI-EAS337_3:7:1:647:1863/2\n-WWWWWWWWWWWWWWVWWWWWWWWVWVWWWWVVVVVS\n-@HWI-EAS337_3:7:1:263:1275/2\n-CAATAACTGGAGCGATGTTAGTAACTGCTGACCACA\n-+HWI-EAS337_3:7:1:263:1275/2\n-WVVWWWWWVVVVWWWWWVWWVWWWWWVWWVTTTTTS\n-@HWI-EAS337_3:7:1:1112:215/2\n-TAACTAAGATATAGGTATACTCTCTCTACATACAAC\n-+HWI-EAS337_3:7:1:1112:215/2\n-VWVWWWWVVVVWWVVWWWVWVVWVVVWWWVTTTTTR\n-@HWI-EAS337_3:7:1:319:1275/2\n-CATTATGTACAAGGATTGAACCTGGTTTGGAACAAC\n-+HWI-EAS337_3:7:1:319:1275/2\n-WWWVWWVWWWVWVVWWWVWWWWWVVVWWVVTTTTTR\n-@HWI-EAS337_3:7:1:1310:1480/2'..b'A\n-+HWI-EAS337_3:7:1:986:591/2\n-WWWWWWWVVWVWWVWWVWWVWWVWWWVWWWTTTROR\n-@HWI-EAS337_3:7:1:181:1099/2\n-CAAGTGAATCCCCATGACAGCATGGAGTAAGAAGGT\n-+HWI-EAS337_3:7:1:181:1099/2\n-WVWWWWWWWVWWWWVVVWWVWVWWWVWVVVTTTTTR\n-@HWI-EAS337_3:7:1:509:832/2\n-AGAGATCAAGACTCTTCAATCACTACGTTGTGGATG\n-+HWI-EAS337_3:7:1:509:832/2\n-VVVWWWWWVVVWWWWVWVVWVVWWVVVVWVTQQSTP\n-@HWI-EAS337_3:7:1:510:597/2\n-TGAATAGGTCGCTGGTATTGCTTCCTGTGGGGTTTA\n-+HWI-EAS337_3:7:1:510:597/2\n-WWWWWWWWWWWWWWWWVWWWWWWVWWVVVVQRTTTR\n-@HWI-EAS337_3:7:1:1765:1489/2\n-AAGAAAATGAATGGATGTGTAATATATGCTATGCAT\n-+HWI-EAS337_3:7:1:1765:1489/2\n-WWVWWWVWWWVVWWWVWVVVWVWWWWWVWWTTTTTR\n-@HWI-EAS337_3:7:1:417:1560/2\n-ATTTACACTATAATATTTATTTTTAAGACTTATGGA\n-+HWI-EAS337_3:7:1:417:1560/2\n-WVWWWWWWWWWWWWWWVVWVWVWVWVVWWWTTTNQS\n-@HWI-EAS337_3:7:1:1047:854/2\n-GAGCTTTCCATGTTTTGACTTCTTCTTTACTACTAA\n-+HWI-EAS337_3:7:1:1047:854/2\n-WWWWVWWWWVVVWWWWVVWWWWWWVWWWVVTTTTTN\n-@HWI-EAS337_3:7:1:1296:202/2\n-AGCTAGAAAGCATCAAATGCACATTTATACTAAATA\n-+HWI-EAS337_3:7:1:1296:202/2\n-VWWWWWVWWWWWWWWVVWWWWWWWWVWWWVTSTTTS\n-@HWI-EAS337_3:7:1:502:642/2\n-ATACATCACTGTGTTACCTAAAAAGAGATTACAAGA\n-+HWI-EAS337_3:7:1:502:642/2\n-WVVVWWVWWVWWVWVVWWWOWVVVVWVLVWTTTTTN\n-@HWI-EAS337_3:7:1:82:1651/2\n-GCTAAAAAGTACTATTTCAAAGAAGGATGAAGAGAT\n-+HWI-EAS337_3:7:1:82:1651/2\n-WWWVWWWWWVVWVVWWWWWWWVWVVVVWWWTTTTTS\n-@HWI-EAS337_3:7:1:1505:1274/2\n-CAACAAACAACACCCAACTCATTCATATATAGTAGC\n-+HWI-EAS337_3:7:1:1505:1274/2\n-WVWWWVVWVWWWWWWVWWVWVVWWVVVWVWTTTTTS\n-@HWI-EAS337_3:7:1:5:1770/2\n-ATGAACTTCAGATATATGGCAACAGACTTAATTAGA\n-+HWI-EAS337_3:7:1:5:1770/2\n-WWWWWWWWWWVWWWWWWVVWWWWVVVWWWVTTTTRS\n-@HWI-EAS337_3:7:1:115:1005/2\n-TGTCCTAAATACTTACAGCAGCTGGGATGGTTTTCC\n-+HWI-EAS337_3:7:1:115:1005/2\n-WWWWWWWWVWWWWWVWWVWVVWWVWVVWVVTTTTTR\n-@HWI-EAS337_3:7:1:354:1708/2\n-GAATCCTTCGTCACAACGGTGAAAGTTGACGGAGCA\n-+HWI-EAS337_3:7:1:354:1708/2\n-WWWVWWWWWVRWVWWVWVWVVVVWWWWWVVTTTTTR\n-@HWI-EAS337_3:7:1:1639:1500/2\n-AACTTTCTAAATATTCGATAATCAATTCTCCAATAT\n-+HWI-EAS337_3:7:1:1639:1500/2\n-WWVWWWWWVWVWWWWWVVWVVWWVVWVWVVTTTTTS\n-@HWI-EAS337_3:7:1:766:243/2\n-TATTACAGTAAGACAAGAACTTCAAGAAGCTTTAGA\n-+HWI-EAS337_3:7:1:766:243/2\n-WVWWWWWVVWVVVWWWVVVWWVWVVVVVVVTTTTRR\n-@HWI-EAS337_3:7:1:920:144/2\n-ATATTTCAGTGGAAACACAAAAATCCAAGGAAGAAA\n-+HWI-EAS337_3:7:1:920:144/2\n-WVWWWWWVVNWVWVWVWVWVVWVRVVWWVVTTTTTR\n-@HWI-EAS337_3:7:1:389:268/2\n-CCAACAGAGAGAAAAGGGAATTCTTTGAGGGTACCT\n-+HWI-EAS337_3:7:1:389:268/2\n-WWWWWVWWWWWWWWWVWVWVWVWWWWVWVVTTTTTS\n-@HWI-EAS337_3:7:1:294:1868/2\n-GGAACATCATTTCACACTTTCAAACACTTAGCAACA\n-+HWI-EAS337_3:7:1:294:1868/2\n-VVWVVVWWWVWWWWVVWWVWVWVVVVWVVWTTTTTR\n-@HWI-EAS337_3:7:1:1147:62/2\n-TAGTTCTCCAGGTTCGGCAACCACAAATACATCATT\n-+HWI-EAS337_3:7:1:1147:62/2\n-WWWWWWWWWVWVVWVVVWVWWWVVVVVVVWTTTTTR\n-@HWI-EAS337_3:7:1:787:1759/2\n-CTGGATTATTATATGATGATATTTGAACTTTCCTTA\n-+HWI-EAS337_3:7:1:787:1759/2\n-VWVWWWWVWWVWVWVWVWWWWWWWVVVVWVTTTTTR\n-@HWI-EAS337_3:7:1:425:1939/2\n-TAACTTTTCTATCTGGTTTCTATGTTTTCCAGCTCT\n-+HWI-EAS337_3:7:1:425:1939/2\n-WVWWWWWWWWWWWWVVVWWWWWWUVWVWVVTQTTTS\n-@HWI-EAS337_3:7:1:187:1132/2\n-GAATAAAAAAAGACAACAACATATCAAGATACAAAG\n-+HWI-EAS337_3:7:1:187:1132/2\n-WWWVWVWWWWWVWWVWWWVWWVWWWVWWVWTTTTTR\n-@HWI-EAS337_3:7:1:1739:1840/2\n-AAAACTGTCCTTCCCGTCAAACTTTTGGGTCAAAAG\n-+HWI-EAS337_3:7:1:1739:1840/2\n-WWVWWWWWWWWWWWWVWWWVVWVCWWVVVVTTTTTR\n-@HWI-EAS337_3:7:1:1505:1876/2\n-CATTCTCTAAACTAGTGAACTTGACAACACTTGATC\n-+HWI-EAS337_3:7:1:1505:1876/2\n-WWWWWWWWWWWWWWWWVWWWWWVWVVWVVVTTTTTS\n-@HWI-EAS337_3:7:1:447:192/2\n-GTGAGTGAAACATATCCAAAAGGCATCTGTTCAGTT\n-+HWI-EAS337_3:7:1:447:192/2\n-WVWWWVWWWWWVWVVWWWVVVVVWWVWVVWTTTTTS\n-@HWI-EAS337_3:7:1:21:2019/2\n-ATTATGTTTACGGGACAATTGTATGTTCCATTATCT\n-+HWI-EAS337_3:7:1:21:2019/2\n-VWVWWWWWWWWWWWWWWWWWVWVWUWVVWWTTTTTR\n-@HWI-EAS337_3:7:1:1593:652/2\n-TTATTTAGCTGTATAATTCCTCTTGTTTTAAGCATA\n-+HWI-EAS337_3:7:1:1593:652/2\n-WWVVWVWWWWWWWVWVVVWVWWWWVWWWWWTKTTTS\n-@HWI-EAS337_3:7:1:1254:1660/2\n-AGTAATGGCATCACATATGGGTAGGAAAAATGTACA\n-+HWI-EAS337_3:7:1:1254:1660/2\n-WVWWWVWVWVWVVWVWWWVWWVVWWVVVVWTTTTTS\n-@HWI-EAS337_3:7:1:291:629/2\n-ATGAAGGGTTTTTTTGTTCTCTAATGTCATCTTATT\n-+HWI-EAS337_3:7:1:291:629/2\n-WWWWVVWWWWWWWWWVWWVWVWVVVQWVVWTTTTTS\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/bamFile.bam |
| b |
| Binary file SMART/data/bamFile.bam has changed |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/dummy.fasta --- a/SMART/data/dummy.fasta Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ ->HWI-EAS337_3:7:1:415:1217/1 -GATGTGCAGACTTTTCACGCAGGACTACATCACTGT ->HWI-EAS337_3:7:1:208:1489/1 -GGAAACATATGCACATAAACGTTGAAATCATGCTTA ->HWI-EAS337_3:7:1:1154:1517/1 -GAATGTTGCAGACCTTACTCCTACCTATGAAGCACA |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/expRef.fasta --- a/SMART/data/expRef.fasta Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,33148 +0,0 @@\n->C10HBa0111D09_LR276\n-GAACAAACAACCCCTTTTTGGAGGTGTTGGCGCGTCGTGCAGCTTACACTCAAAAGTTAA\n-AAAGTTGCCTTGCGATGCGGTCATGTTACAAACCTCTCTGCCTTAAATTAAATTCCATAA\n-CCAAGATTTGGAGGTGCCTCAACGATGCGCAGCCATGTCCCATATTTGGTCGCCTCGTTT\n-AAAAGTCAAGTTAGACTTAATTAAGAGGTCCAACTAGTGTAGGGGCGTTTTGAGTACTTG\n-TGGGATTTATTATAAACGGTTTTGAGTCACTTTAAACCCACTTCACCAATTAAAACAAAA\n-TCCTCAAGTTAAAACTCAATATCTTTCCATTCTCTCTCTCTAAAACCTTCATTGGAGATA\n-TTTGAAGCTCCACGGAAGAAGGTTAATTTTCCAAGGTTTCAATGAAAATTTCGTGTATAG\n-GTCTTCAATAAGGTATGGTGATTTCATCCTTGATTCTTCTATCATTCAAGGATCCAATTC\n-AAAGGTTTTTCAAAAGATCTCAAAAATCCTATTTCGAATTCTAAGTATGGGTTCTTCCAT\n-TTAAAGGTTTAAATGGATGAATTATGATGTTTTCAATGTTAGTTGATGTTTTTATGATAA\n-AAAAACTCCATGAACCCATGAGCATCCTAATTCTCTAATTTTGTCTTGTAAATTGAGTTT\n-GATAATTGTGATTGGTTATGGATGGAATTGTATTTAGATTGCTCTATATTGTTGATTCTT\n-ATTGTTAACCTATCTCTATATATGTAGAATTGAGATTGTAAGGATGAGTTAGTAATCTTG\n-GCTTTATGGGCTTTCGAATCCGGGTTTACCCCCTGGATGTAACCGGCATCCTCGCCCTTT\n-TTCAAGGACTAAGACCAACCTTTTAGTCTCATGTCATTACATTCATAGGTTGACAAATGC\n-GGAAAAATTTAAAACTTTCATTATCACTACTTGGAGGTTTACATAGACCTCTACATACAC\n-ATAAGATATATTCATATAGAGTATACATAGACCCTTCGTATAGGAAGGTTACATAGCCAT\n-CTACTTTTATTACACATACATATATATAAAATATAAAAATAGTCTAACGATTGTCTCATC\n-TCATACCCTCTAAACGATTATCACAATATGGGCATAACCCTTACATCAATCAAACAAGAG\n-CACATATAGGTCATACAAAAGTATAGTACTCAATTAAAAAGGAAAGAAATGAAAGAGTCT\n-TTAAGCTCATAACAAGTCCATAAGCTAGATTATGGCATTGACCTCAAAAGTTGAGGACCT\n-TATGTGCGTACACAAGCAAAACATGCTAAAAAGGGACTTTTTAGTCAAAACATGCCCATT\n-TATCCCTTTAAGAACCTACTACAAAGCCAACAAGTCATACCAACCAACCAAACATGCTTA\n-CTATCTCAACAAGTAATACTTATCCCAACATACTTGAAACCATGATTTACTACAACCCTA\n-TCACCAAGGAAAAATATCACAAGAATGAATAAGAGTCAATCATATCATGATAGAGAGACA\n-ACTATTCATGAATCCTTATCAACTCAACAAGTGCAATAACCAAGCAAAGCCTCATAACCT\n-TACTCAATCAAGTATCCTCAAAAAGAAACCATGACCAATGTCCAACTTTACCTAACATAG\n-CATTTAGGTTTACATTTTATCATATATTAACATTATGACCCAAGGCATACTCATTAGTAA\n-ACTAATTAATATATAATATCAACAATGTGCCATAGTAATCATATATACATAATATATCAT\n-CATAACATAAACATATATAAAAACCTCCTTCTAAGACTCCCCTCAAGGCTAACTAGTGAA\n-ATGTTTAGGTAGAGCCCCATACCCCTACCTAGATTAAGCTAGACCCCTTAGGTTATCCAA\n-GTTAGAGTTCAAGTCCTTTAATTCGTTTTACCTTTTGGGAACATCTTGCCCTAACCGACA\n-TAGACCACATGAGCTAGTGTGGGATACGGTTCCAAAAAACCCTACACAGAAAGAAGGCGG\n-ACTACTTGCCAAAGTATTACCAAAACATGAAACATAGCAACTACGTTGATCCACTAGCAA\n-GTATTTCTATAGGGGCAACATAGTTCAAGAACTCTGAGATATACTTGAGACCCTCTTTAT\n-GCGCCATGCATTATAGTCTCCAACCTCAAGAGTAATGTAGTGTTCCTACCTTCCCCATGT\n-GAGAAAGGACACTCCTCAATCTAGTTCACTCGGTGCTAAGCTAGAGACCCTTTTTGAAAT\n-GTCTTTAAGCCTTTAATTATCAATCATAGCTTAGCTTAGGTCATAGGGTATATCTCTTGT\n-ATAATCATCATCATCAATAGCTCAATAATAATTGTATGAGTATAAGTCCTTTCATCACAA\n-TTCATATAAGTGAGGTTAACATGTTAGCATTTCATTGCATATCAAGAAACATTGATGATT\n-CTTACCATCCTTGTATCACATACACCTTAATCAATCTCACAACATAGTCAGGACATATCA\n-ATTCAACATCATACCACCCTATAATCCTAATATAAGGCATACTCCAATATAACTTCACGT\n-CTTAACAAAAATTTATCACAATTGGAATTAAAGATAGAGATTCTAAGACTTAACAAGTCT\n-TCCTTGTAGTTCATCATCAAGGTCTTACCATCAACCCATAACTCAACCAAGTTTGGGGAG\n-TAACATCATCACACAATGATAATCAATAGGATAACAAGGCTAATTTCATCTCTATAACAC\n-AATTCAACACTAGATCATAACTTAAGACAAGATACATAGGCTAATTTCACACTATAATTC\n-ATAACCTAAATCACATCTCAAGAAATAGCATTATAGTCCTATAATTCATATTAATTTGTT\n-CATAATAACACAATAGGATAGTAATTTAATCAATAACCAAGTCAATTGAATGATCACAAT\n-ACAATATACATCAATATCACAAGCTAGGGTTAGGGATGAAGGATCATATTCTTCAATTTA\n-GACCAAACCACTAACAATTACCATAATAAAGTTTAAATTCATGTAAATGTATTCAATATA\n-ACCTAAATAAATCATTAACAACTCAATCCATAACTTCAATTTCGTAATTGAATGAAACCC\n-ATAAGAAAATTCACCTTTTGAAATCCATTTTAAAGAAACCCTTTGAGGAAAGAGCCTCAA\n-AGGTGAATTAGATCCCATATATTAATGTTTGATGATGAATTCGCCCCTTTCCATCCCCCA\n-AACCCTTATCCTTGCTAGTTTTTAATGGTGAGTTCAAGTAGAGAGAGAAATAAGAGAGAA\n-GGAAGAGAGTTTTTGTCTTAGAGTTCTAATTAATTTAATTGGGGTTGGGGATTTTATATG\n-CGTTTTAAGTTAGTTAATTAGTCACCCCTCAATACCTAACTAACCCCTGAACCACCTAAT\n-TAATTAAATGAATCAATATAAAAACATACAGGAAATTTGACCTTCACAGACGAGACCCCG\n-AACGACGGGCCATCTGTGAGTCAACGGTCCCTCACCCCTCCGTCCTGCACTCTATCGATC\n-AGTTCATAGACTGTGCAGGCAGATCAATTCTTCAACTTGTCTAAGTATGGGATGACGGTG\n-GTATCGACTCCCCGTCAGTCCACACACGGACCGTAGGTGGTCCCATCGATGCGCATTGTC\n-TAGTCCTTGTTTGTTCAAACACAAGGGCCTCAAGGGCCCTTGGTTGGTGCTTGGGGAGTC\n-GTACCCATACGTTTCAATCATGAAACAACTCAAAAACCTATAATCTATCCTTCCACCAAT\n-TTTTGTACCTTTCCGACTCTTAAAAGGTAGTCAAATAGGCTAAGGCACGCTAACACCCCT\n-TTGAACCAACTTCCTGGACGTTCTTATACATTTTGGTTCTTAAACTTCCT'..b'CAATATTCCATATTGATCGCCAGCTTCCATTGCTACAAAAGA\n-TGCATATAGTATCAGCTTCTTTAGACAAAGCTATAAGAAGTATCAGTTGACCCAATTGAC\n-AAGTCACACGTGCTATAACAAGATATCACTTGACGCAAGTGACAAGTGTGAAGCTGACAG\n-GAAAATAGGCAATAGAATCCCTCATTCTTTGTTTATATATAGCAACCTATTACTTCAGTA\n-TCTGTTTACAAGTTCTGCACCACGATAAGTATAACTATTTAGAAATTATGAAGGGAGTGT\n-TGCACAAATTAGTCAGGGTTAGAATTTTAATAATCCAACACACCAGAAATTCTGAGGACT\n-ATGCCTAGCAGCTGAAATCACCACAACAAGTTCAAAGTCAAATCCTGGCTCTTCCACATC\n-CTTTCCCTTCGTACAGTAAACTGAACAGATGCCTTTTGGATATGTTTCACTCACATACTT\n-CATAATTTCAGCATCCATGGCAGACCTACACAAGAATTACCATGAATAGGAGAATTTGGC\n-AAGCAACGGTAATCACAAAGTCAGTACTCATAAACCAAGCCTCTGATGAGAAGAACTAAC\n-CATGTTAAGAAGGGAACTACTCACATAAAACAAAAACATGATTTTTATAATCTGCATGCC\n-AAGCATTAGGAACTATTGAAGAATTCACTGCGATCTCAGAATATAATCCTTTCATACTCT\n-TAATGCCTCCCAATTATACCAAATTTAGGTGTCTTACTACCATTTTAGTATCTGACATTG\n-ATGTCATTACCCATTAATTTGGAGACACTGGTTCCTCACCGATAAAGATGAACAAAAAGG\n-TAAACCAGTGTATTATGAATCAGATCTCTTTATGGAATAAAAACACACATGAATCATGAT\n-GTAGGATCTTATTAACACTTGAGGACTGAGGCGAAGATTACTAAGAATATCCCGAAAGAT\n-AAGACATAGAATGTAATATAGAAGGACAGAGAACAAATGATACTGATTAAGAAGAAGAGC\n-ATCTATATAGGAGAGATTAGCCTAAACTATTTATTTTCAGACTGATTTCGGTGAGCGCAG\n-ACCAAAACATGCAGCTTTTTTTTCAATTAAGCCGGAAAGACAATTTCCACAAGAAATGCA\n-ACTGTTCTAGCATATCTTAAACTATAATCTGAGTGCTGTCTGAGAACTGAGGTTGAATTT\n-GCAAGTCTTGTTGAGCATGGTTAAAAAATAAGTCCAATTAGGCAAAATAATTGTGAATGT\n-CATAATATAGAAGAACTTCAACATCTCAATGGGAAAAACAGAAAGTGAGTAGCTAAAAAG\n-GGGAGCAATACCAAAGATATTAAACTGAGAAATATATCTCATACCCTACAGATGCATACC\n-TATACTCTTCCACGAAAGCAGATGGAAGTTCTTCATCTCTTGCTGGCCTAACGTCTTTAC\n-AAACCTAGAATGCAGACATACCATGAGCTTACAAGAAGGGAGCATAAATTATTACACGGC\n-AACAATAACTAGGAAAAAAAGAGAGAGAGGAAATACATTTAATTTCACAGCCCTTGAATT\n-ATGAATAAAACCATGCACTTGTTATATTAAGCAGAGACTACTTCCACTTTTCCAATCTAT\n-TTACATCTACTTCATCACATTAACAAGAATAGAAAAGAAATGCATGTTATGTGACATTCA\n-GCACTGTAGACTAATGAGGATTAATTTACAACCATGGACCAGCTATAGCAGAAGAGACCT\n-TATTTTACTTTTCCAAAATTGGTATTTACTCCATCACCATTAACAAGAATAAAAAATGCA\n-TCTTATGTGAAGTTCATAACTATTGAATAATGAGGTTAATCAAGAGCTTGCTATATCAAA\n-GCACATTTTTCAAGTTTACAATTTCTTCATTCTTGGTATCCACTTCTATCATGAAAACCA\n-ACCTAACAGTTAACACAATTCACTCTGGTGTTTTGTTCTTTATCCCTAATGCCTGAGTGT\n-GTTTAACTAATCAAGTTCCAATCAGCCAGAAGATGTCTAAACATACTAAACTATAGATAA\n-ACAACATGAGCATAAAACCAGTTTATGTAGAGATTTTTAATTGCACAGCATAAAAAGGAG\n-TACCCCCGGCACTATATGTGCTTCTCTTTCTTTTTTTCTTACTTCGTCCTGATCTTTTTA\n-CTTTTCTTTTCCTTTCTTTCAGAATAAGCACATTTTTGGATATAGTCCCACCATCTCTAC\n-CAGGTTTATGTCTGTCCATATTATTGCTTTTTTGAATTACCTTCTAAACAAAATACTCAT\n-CCTTACAAACCTGCTTCCTCTTCTATGGATCCCACCACTCCATGCCCCGAAAAAAAAGAA\n-AGAAAAAGATAAGTTTTTCATAGTCACTTTAGATTATCATTTATTAAATTCTGTCGGCTC\n-AACTGATAGGAACAGTGAAATGGACTTTTCAATCATAAAAAGATAATAGAAGTTATTAAA\n-TGATTCCCTTCAAGATTATGAGCTTTTAAACTTACATATCATGCAACTATTGGGGAATTA\n-AGGGACTGGGGATTTGATGATAAATTCCAGCACCATTTTTGGTGCTTTTGTGTTTTTGCA\n-AGGTAGTTTGTTAGTGGCACATGGAAGGAGGTGCCTCATCCAATGAAATTATTAATCTTA\n-TCAACAAGAAGAAAGTCAAAACACCAAACTGTAAAAAATCCAAAAATAGCATTTTGCATT\n-GTGTACTAACTGAACAACGTACTTGCTTGACATGGTCAACTCTGGCAACCTGCGCAGTCC\n-GGGGATCAAGATACTCATCCTTATGAACCTCACTAAATGATGTAATCAGTACCTACAAAT\n-TAGTGAACAGCAACTTTACACAGCTAGATCATGAAAAATAGCTTCCAAGTGTCCATTACT\n-ACATAAATGAAAAGCATTATACTTTCTTTTTAGAAGAGGGGAACAAAATCTTAGACTTCA\n-TAAGGAACAGTTCTCCGGAAAGTTTTCTTTTCTATATTGAAGAAGTAATCATTTATTGAA\n-GTGGTGGAAATTCCCTAAGCTTTAAACAGATGTAGAGAACTTGTCCATAAACATGGTGCT\n-CAACAAACAACACCCAACTCATTCATATATAGTAGCGCCAGCATCCAAGTACCATGAAGT\n-ATATCTCTATCCTAAAAGCTTTACTTGAAGACTTATTAGATTAATCTTACTTATTTCTCA\n-TGCAACTTTTTTTTTGAAAAGTTTCTCAAGCATAACTTTTATCCTTTGTTTTCATTCAGT\n-CTTTGAGCTCTAAAGGATGCCTAGAGAGGTCATGAACCAAGTAAGGAAATTGCAACATCA\n-TATTGCTTCCAATTTACCTCATTTTTTATCTTCAACTACCGAAAACTACCAAATCTGAAA\n-TTATCAACTAAGGAAAATTACAACATCAGTACAATAAGTATTGCTTACAGTTCACTTAAT\n-ATTTCAATCTTCGACTACGGAAAACTGTCAAATCTGAAATTATCAATTTGAATGACACGA\n-TTAGTCTAACTTACATTTTCAAAGATCTAACTTACCCAATGAAAAAAGAAAACAAGAGAG\n-AGACTTACATCGCCACTTCTGTTTGGGAATTCGAGACAAATCAAGTGAGATTTGTTGTAC\n-GAAGGAAATGACTCCTCGGCCGCTTTCTTATATATATTTTCGTCCTTTAAAATAGCTCTA\n-ACATCTGCAAATCCAACCAAATGACGCTCAAAACCAAAAATGTAAAAAATAAACTGCCGA\n-TCGCAAATGAACACCAATGCGGTCACATTTTCAAGCACGAAAAAAGCTTCAAAATACAAA\n-AAACTTTAGCGCAGAAAATAAACGAAAGAGAAGAAGAAGAAGACCTTTGGCGACGTACTG\n-AATTTCGCCGGCTGGGGCATTAAGAAGGAACCATTTGGCAATCTCAAT\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/expRef_withoutSplit.fasta --- a/SMART/data/expRef_withoutSplit.fasta Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,33148 +0,0 @@\n->C10HBa0111D09_LR276\n-GAACAAACAACCCCTTTTTGGAGGTGTTGGCGCGTCGTGCAGCTTACACTCAAAAGTTAA\n-AAAGTTGCCTTGCGATGCGGTCATGTTACAAACCTCTCTGCCTTAAATTAAATTCCATAA\n-CCAAGATTTGGAGGTGCCTCAACGATGCGCAGCCATGTCCCATATTTGGTCGCCTCGTTT\n-AAAAGTCAAGTTAGACTTAATTAAGAGGTCCAACTAGTGTAGGGGCGTTTTGAGTACTTG\n-TGGGATTTATTATAAACGGTTTTGAGTCACTTTAAACCCACTTCACCAATTAAAACAAAA\n-TCCTCAAGTTAAAACTCAATATCTTTCCATTCTCTCTCTCTAAAACCTTCATTGGAGATA\n-TTTGAAGCTCCACGGAAGAAGGTTAATTTTCCAAGGTTTCAATGAAAATTTCGTGTATAG\n-GTCTTCAATAAGGTATGGTGATTTCATCCTTGATTCTTCTATCATTCAAGGATCCAATTC\n-AAAGGTTTTTCAAAAGATCTCAAAAATCCTATTTCGAATTCTAAGTATGGGTTCTTCCAT\n-TTAAAGGTTTAAATGGATGAATTATGATGTTTTCAATGTTAGTTGATGTTTTTATGATAA\n-AAAAACTCCATGAACCCATGAGCATCCTAATTCTCTAATTTTGTCTTGTAAATTGAGTTT\n-GATAATTGTGATTGGTTATGGATGGAATTGTATTTAGATTGCTCTATATTGTTGATTCTT\n-ATTGTTAACCTATCTCTATATATGTAGAATTGAGATTGTAAGGATGAGTTAGTAATCTTG\n-GCTTTATGGGCTTTCGAATCCGGGTTTACCCCCTGGATGTAACCGGCATCCTCGCCCTTT\n-TTCAAGGACTAAGACCAACCTTTTAGTCTCATGTCATTACATTCATAGGTTGACAAATGC\n-GGAAAAATTTAAAACTTTCATTATCACTACTTGGAGGTTTACATAGACCTCTACATACAC\n-ATAAGATATATTCATATAGAGTATACATAGACCCTTCGTATAGGAAGGTTACATAGCCAT\n-CTACTTTTATTACACATACATATATATAAAATATAAAAATAGTCTAACGATTGTCTCATC\n-TCATACCCTCTAAACGATTATCACAATATGGGCATAACCCTTACATCAATCAAACAAGAG\n-CACATATAGGTCATACAAAAGTATAGTACTCAATTAAAAAGGAAAGAAATGAAAGAGTCT\n-TTAAGCTCATAACAAGTCCATAAGCTAGATTATGGCATTGACCTCAAAAGTTGAGGACCT\n-TATGTGCGTACACAAGCAAAACATGCTAAAAAGGGACTTTTTAGTCAAAACATGCCCATT\n-TATCCCTTTAAGAACCTACTACAAAGCCAACAAGTCATACCAACCAACCAAACATGCTTA\n-CTATCTCAACAAGTAATACTTATCCCAACATACTTGAAACCATGATTTACTACAACCCTA\n-TCACCAAGGAAAAATATCACAAGAATGAATAAGAGTCAATCATATCATGATAGAGAGACA\n-ACTATTCATGAATCCTTATCAACTCAACAAGTGCAATAACCAAGCAAAGCCTCATAACCT\n-TACTCAATCAAGTATCCTCAAAAAGAAACCATGACCAATGTCCAACTTTACCTAACATAG\n-CATTTAGGTTTACATTTTATCATATATTAACATTATGACCCAAGGCATACTCATTAGTAA\n-ACTAATTAATATATAATATCAACAATGTGCCATAGTAATCATATATACATAATATATCAT\n-CATAACATAAACATATATAAAAACCTCCTTCTAAGACTCCCCTCAAGGCTAACTAGTGAA\n-ATGTTTAGGTAGAGCCCCATACCCCTACCTAGATTAAGCTAGACCCCTTAGGTTATCCAA\n-GTTAGAGTTCAAGTCCTTTAATTCGTTTTACCTTTTGGGAACATCTTGCCCTAACCGACA\n-TAGACCACATGAGCTAGTGTGGGATACGGTTCCAAAAAACCCTACACAGAAAGAAGGCGG\n-ACTACTTGCCAAAGTATTACCAAAACATGAAACATAGCAACTACGTTGATCCACTAGCAA\n-GTATTTCTATAGGGGCAACATAGTTCAAGAACTCTGAGATATACTTGAGACCCTCTTTAT\n-GCGCCATGCATTATAGTCTCCAACCTCAAGAGTAATGTAGTGTTCCTACCTTCCCCATGT\n-GAGAAAGGACACTCCTCAATCTAGTTCACTCGGTGCTAAGCTAGAGACCCTTTTTGAAAT\n-GTCTTTAAGCCTTTAATTATCAATCATAGCTTAGCTTAGGTCATAGGGTATATCTCTTGT\n-ATAATCATCATCATCAATAGCTCAATAATAATTGTATGAGTATAAGTCCTTTCATCACAA\n-TTCATATAAGTGAGGTTAACATGTTAGCATTTCATTGCATATCAAGAAACATTGATGATT\n-CTTACCATCCTTGTATCACATACACCTTAATCAATCTCACAACATAGTCAGGACATATCA\n-ATTCAACATCATACCACCCTATAATCCTAATATAAGGCATACTCCAATATAACTTCACGT\n-CTTAACAAAAATTTATCACAATTGGAATTAAAGATAGAGATTCTAAGACTTAACAAGTCT\n-TCCTTGTAGTTCATCATCAAGGTCTTACCATCAACCCATAACTCAACCAAGTTTGGGGAG\n-TAACATCATCACACAATGATAATCAATAGGATAACAAGGCTAATTTCATCTCTATAACAC\n-AATTCAACACTAGATCATAACTTAAGACAAGATACATAGGCTAATTTCACACTATAATTC\n-ATAACCTAAATCACATCTCAAGAAATAGCATTATAGTCCTATAATTCATATTAATTTGTT\n-CATAATAACACAATAGGATAGTAATTTAATCAATAACCAAGTCAATTGAATGATCACAAT\n-ACAATATACATCAATATCACAAGCTAGGGTTAGGGATGAAGGATCATATTCTTCAATTTA\n-GACCAAACCACTAACAATTACCATAATAAAGTTTAAATTCATGTAAATGTATTCAATATA\n-ACCTAAATAAATCATTAACAACTCAATCCATAACTTCAATTTCGTAATTGAATGAAACCC\n-ATAAGAAAATTCACCTTTTGAAATCCATTTTAAAGAAACCCTTTGAGGAAAGAGCCTCAA\n-AGGTGAATTAGATCCCATATATTAATGTTTGATGATGAATTCGCCCCTTTCCATCCCCCA\n-AACCCTTATCCTTGCTAGTTTTTAATGGTGAGTTCAAGTAGAGAGAGAAATAAGAGAGAA\n-GGAAGAGAGTTTTTGTCTTAGAGTTCTAATTAATTTAATTGGGGTTGGGGATTTTATATG\n-CGTTTTAAGTTAGTTAATTAGTCACCCCTCAATACCTAACTAACCCCTGAACCACCTAAT\n-TAATTAAATGAATCAATATAAAAACATACAGGAAATTTGACCTTCACAGACGAGACCCCG\n-AACGACGGGCCATCTGTGAGTCAACGGTCCCTCACCCCTCCGTCCTGCACTCTATCGATC\n-AGTTCATAGACTGTGCAGGCAGATCAATTCTTCAACTTGTCTAAGTATGGGATGACGGTG\n-GTATCGACTCCCCGTCAGTCCACACACGGACCGTAGGTGGTCCCATCGATGCGCATTGTC\n-TAGTCCTTGTTTGTTCAAACACAAGGGCCTCAAGGGCCCTTGGTTGGTGCTTGGGGAGTC\n-GTACCCATACGTTTCAATCATGAAACAACTCAAAAACCTATAATCTATCCTTCCACCAAT\n-TTTTGTACCTTTCCGACTCTTAAAAGGTAGTCAAATAGGCTAAGGCACGCTAACACCCCT\n-TTGAACCAACTTCCTGGACGTTCTTATACATTTTGGTTCTTAAACTTCCT'..b'CAATATTCCATATTGATCGCCAGCTTCCATTGCTACAAAAGA\n-TGCATATAGTATCAGCTTCTTTAGACAAAGCTATAAGAAGTATCAGTTGACCCAATTGAC\n-AAGTCACACGTGCTATAACAAGATATCACTTGACGCAAGTGACAAGTGTGAAGCTGACAG\n-GAAAATAGGCAATAGAATCCCTCATTCTTTGTTTATATATAGCAACCTATTACTTCAGTA\n-TCTGTTTACAAGTTCTGCACCACGATAAGTATAACTATTTAGAAATTATGAAGGGAGTGT\n-TGCACAAATTAGTCAGGGTTAGAATTTTAATAATCCAACACACCAGAAATTCTGAGGACT\n-ATGCCTAGCAGCTGAAATCACCACAACAAGTTCAAAGTCAAATCCTGGCTCTTCCACATC\n-CTTTCCCTTCGTACAGTAAACTGAACAGATGCCTTTTGGATATGTTTCACTCACATACTT\n-CATAATTTCAGCATCCATGGCAGACCTACACAAGAATTACCATGAATAGGAGAATTTGGC\n-AAGCAACGGTAATCACAAAGTCAGTACTCATAAACCAAGCCTCTGATGAGAAGAACTAAC\n-CATGTTAAGAAGGGAACTACTCACATAAAACAAAAACATGATTTTTATAATCTGCATGCC\n-AAGCATTAGGAACTATTGAAGAATTCACTGCGATCTCAGAATATAATCCTTTCATACTCT\n-TAATGCCTCCCAATTATACCAAATTTAGGTGTCTTACTACCATTTTAGTATCTGACATTG\n-ATGTCATTACCCATTAATTTGGAGACACTGGTTCCTCACCGATAAAGATGAACAAAAAGG\n-TAAACCAGTGTATTATGAATCAGATCTCTTTATGGAATAAAAACACACATGAATCATGAT\n-GTAGGATCTTATTAACACTTGAGGACTGAGGCGAAGATTACTAAGAATATCCCGAAAGAT\n-AAGACATAGAATGTAATATAGAAGGACAGAGAACAAATGATACTGATTAAGAAGAAGAGC\n-ATCTATATAGGAGAGATTAGCCTAAACTATTTATTTTCAGACTGATTTCGGTGAGCGCAG\n-ACCAAAACATGCAGCTTTTTTTTCAATTAAGCCGGAAAGACAATTTCCACAAGAAATGCA\n-ACTGTTCTAGCATATCTTAAACTATAATCTGAGTGCTGTCTGAGAACTGAGGTTGAATTT\n-GCAAGTCTTGTTGAGCATGGTTAAAAAATAAGTCCAATTAGGCAAAATAATTGTGAATGT\n-CATAATATAGAAGAACTTCAACATCTCAATGGGAAAAACAGAAAGTGAGTAGCTAAAAAG\n-GGGAGCAATACCAAAGATATTAAACTGAGAAATATATCTCATACCCTACAGATGCATACC\n-TATACTCTTCCACGAAAGCAGATGGAAGTTCTTCATCTCTTGCTGGCCTAACGTCTTTAC\n-AAACCTAGAATGCAGACATACCATGAGCTTACAAGAAGGGAGCATAAATTATTACACGGC\n-AACAATAACTAGGAAAAAAAGAGAGAGAGGAAATACATTTAATTTCACAGCCCTTGAATT\n-ATGAATAAAACCATGCACTTGTTATATTAAGCAGAGACTACTTCCACTTTTCCAATCTAT\n-TTACATCTACTTCATCACATTAACAAGAATAGAAAAGAAATGCATGTTATGTGACATTCA\n-GCACTGTAGACTAATGAGGATTAATTTACAACCATGGACCAGCTATAGCAGAAGAGACCT\n-TATTTTACTTTTCCAAAATTGGTATTTACTCCATCACCATTAACAAGAATAAAAAATGCA\n-TCTTATGTGAAGTTCATAACTATTGAATAATGAGGTTAATCAAGAGCTTGCTATATCAAA\n-GCACATTTTTCAAGTTTACAATTTCTTCATTCTTGGTATCCACTTCTATCATGAAAACCA\n-ACCTAACAGTTAACACAATTCACTCTGGTGTTTTGTTCTTTATCCCTAATGCCTGAGTGT\n-GTTTAACTAATCAAGTTCCAATCAGCCAGAAGATGTCTAAACATACTAAACTATAGATAA\n-ACAACATGAGCATAAAACCAGTTTATGTAGAGATTTTTAATTGCACAGCATAAAAAGGAG\n-TACCCCCGGCACTATATGTGCTTCTCTTTCTTTTTTTCTTACTTCGTCCTGATCTTTTTA\n-CTTTTCTTTTCCTTTCTTTCAGAATAAGCACATTTTTGGATATAGTCCCACCATCTCTAC\n-CAGGTTTATGTCTGTCCATATTATTGCTTTTTTGAATTACCTTCTAAACAAAATACTCAT\n-CCTTACAAACCTGCTTCCTCTTCTATGGATCCCACCACTCCATGCCCCGAAAAAAAAGAA\n-AGAAAAAGATAAGTTTTTCATAGTCACTTTAGATTATCATTTATTAAATTCTGTCGGCTC\n-AACTGATAGGAACAGTGAAATGGACTTTTCAATCATAAAAAGATAATAGAAGTTATTAAA\n-TGATTCCCTTCAAGATTATGAGCTTTTAAACTTACATATCATGCAACTATTGGGGAATTA\n-AGGGACTGGGGATTTGATGATAAATTCCAGCACCATTTTTGGTGCTTTTGTGTTTTTGCA\n-AGGTAGTTTGTTAGTGGCACATGGAAGGAGGTGCCTCATCCAATGAAATTATTAATCTTA\n-TCAACAAGAAGAAAGTCAAAACACCAAACTGTAAAAAATCCAAAAATAGCATTTTGCATT\n-GTGTACTAACTGAACAACGTACTTGCTTGACATGGTCAACTCTGGCAACCTGCGCAGTCC\n-GGGGATCAAGATACTCATCCTTATGAACCTCACTAAATGATGTAATCAGTACCTACAAAT\n-TAGTGAACAGCAACTTTACACAGCTAGATCATGAAAAATAGCTTCCAAGTGTCCATTACT\n-ACATAAATGAAAAGCATTATACTTTCTTTTTAGAAGAGGGGAACAAAATCTTAGACTTCA\n-TAAGGAACAGTTCTCCGGAAAGTTTTCTTTTCTATATTGAAGAAGTAATCATTTATTGAA\n-GTGGTGGAAATTCCCTAAGCTTTAAACAGATGTAGAGAACTTGTCCATAAACATGGTGCT\n-CAACAAACAACACCCAACTCATTCATATATAGTAGCGCCAGCATCCAAGTACCATGAAGT\n-ATATCTCTATCCTAAAAGCTTTACTTGAAGACTTATTAGATTAATCTTACTTATTTCTCA\n-TGCAACTTTTTTTTTGAAAAGTTTCTCAAGCATAACTTTTATCCTTTGTTTTCATTCAGT\n-CTTTGAGCTCTAAAGGATGCCTAGAGAGGTCATGAACCAAGTAAGGAAATTGCAACATCA\n-TATTGCTTCCAATTTACCTCATTTTTTATCTTCAACTACCGAAAACTACCAAATCTGAAA\n-TTATCAACTAAGGAAAATTACAACATCAGTACAATAAGTATTGCTTACAGTTCACTTAAT\n-ATTTCAATCTTCGACTACGGAAAACTGTCAAATCTGAAATTATCAATTTGAATGACACGA\n-TTAGTCTAACTTACATTTTCAAAGATCTAACTTACCCAATGAAAAAAGAAAACAAGAGAG\n-AGACTTACATCGCCACTTCTGTTTGGGAATTCGAGACAAATCAAGTGAGATTTGTTGTAC\n-GAAGGAAATGACTCCTCGGCCGCTTTCTTATATATATTTTCGTCCTTTAAAATAGCTCTA\n-ACATCTGCAAATCCAACCAAATGACGCTCAAAACCAAAAATGTAAAAAATAAACTGCCGA\n-TCGCAAATGAACACCAATGCGGTCACATTTTCAAGCACGAAAAAAGCTTCAAAATACAAA\n-AAACTTTAGCGCAGAAAATAAACGAAAGAGAAGAAGAAGAAGACCTTTGGCGACGTACTG\n-AATTTCGCCGGCTGGGGCATTAAGAAGGAACCATTTGGCAATCTCAAT\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/output.png |
| b |
| Binary file SMART/data/output.png has changed |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/part0.bam |
| b |
| Binary file SMART/data/part0.bam has changed |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/part0.sam --- a/SMART/data/part0.sam Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,448 +0,0 @@\n-@SQ\tSN:C10HBa0111D09_LR276\tLN:9300\n-@SQ\tSN:C11HBa0029C01_LR281\tLN:10969\n-@SQ\tSN:C11HBa0034I10_LR282\tLN:9056\n-@SQ\tSN:C11HBa0054I23_LR283\tLN:10301\n-@SQ\tSN:C11HBa0062I24_LR284\tLN:10050\n-@SQ\tSN:C11HBa0064J13_LR285\tLN:9385\n-@SQ\tSN:C11HBa0072I13_LR286\tLN:9556\n-@SQ\tSN:C11HBa0089M02_LR287\tLN:9244\n-@SQ\tSN:C11HBa0096D22_LR288\tLN:9184\n-@SQ\tSN:C11HBa0107K14_LR289\tLN:9115\n-@SQ\tSN:C11HBa0139J14_LR291\tLN:10002\n-@SQ\tSN:C11HBa0143O06_LR374\tLN:10785\n-@SQ\tSN:C11HBa0161D01_LR292\tLN:9057\n-@SQ\tSN:C11HBa0168B23_LR293\tLN:9826\n-@SQ\tSN:C11HBa0190J03_LR294\tLN:10992\n-@SQ\tSN:C11HBa0249E07_LR279\tLN:10008\n-@SQ\tSN:C11HBa0303G16_LR296\tLN:9430\n-@SQ\tSN:C11HBa0323E19_LR297\tLN:9657\n-@SQ\tSN:C11SLe0053P22_LR298\tLN:9827\n-@SQ\tSN:C11SLm0052K14_LR376\tLN:10013\n-@SQ\tSN:C12HBa115G22_LR301\tLN:10021\n-@SQ\tSN:C12HBa120K4_LR313\tLN:10271\n-@SQ\tSN:C12HBa144B17_LR302\tLN:9247\n-@SQ\tSN:C12HBa149G24_LR381\tLN:9271\n-@SQ\tSN:C12HBa165B12_LR303\tLN:9257\n-@SQ\tSN:C12HBa183M6_LR379\tLN:9473\n-@SQ\tSN:C12HBa221M9_LR377\tLN:10755\n-@SQ\tSN:C12HBa224N6_LR382\tLN:9130\n-@SQ\tSN:C12HBa26C13_LR299\tLN:9139\n-@SQ\tSN:C12HBa326K10_LR306\tLN:10414\n-@SQ\tSN:C12HBa90D9_LR311\tLN:9638\n-@SQ\tSN:C12HBa93P12_LR312\tLN:9510\n-@SQ\tSN:C12SLe124D18_LR385\tLN:10545\n-@SQ\tSN:C12SLeRI72J6_LR378\tLN:9337\n-@SQ\tSN:C12SLm103K8_LR380\tLN:10118\n-@SQ\tSN:C01HBa0003D15_LR7\tLN:10776\n-@SQ\tSN:C01HBa0163B20_LR10\tLN:9321\n-@SQ\tSN:C01HBa0216G16_LR11\tLN:10332\n-@SQ\tSN:C01HBa0256E08_LR13\tLN:9024\n-@SQ\tSN:C01HBa0329A12_LR14\tLN:9536\n-@SQ\tSN:BAC19_LR16\tLN:9760\n-@SQ\tSN:C02HBa0008G02_LR67\tLN:9205\n-@SQ\tSN:C02HBa0011O23_LR68\tLN:9399\n-@SQ\tSN:C02HBa0016A12_LR19\tLN:9822\n-@SQ\tSN:C02HBa0027B01_LR21\tLN:9222\n-@SQ\tSN:C02HBa0030A21_LR22\tLN:9147\n-@SQ\tSN:C02HBa0046M08_LR23\tLN:10763\n-@SQ\tSN:C02HBa0072A04_LR26\tLN:9766\n-@SQ\tSN:C02HBa0075D08_LR28\tLN:10744\n-@SQ\tSN:C02HBa0124N09_LR31\tLN:9335\n-@SQ\tSN:C02HBa0155D20_LR36\tLN:10743\n-@SQ\tSN:C02HBa0155E05_LR37\tLN:10417\n-@SQ\tSN:C02HBa0164H08_LR38\tLN:10279\n-@SQ\tSN:C02HBa0167J21_LR39\tLN:9925\n-@SQ\tSN:C02HBa0185P07_LR40\tLN:9818\n-@SQ\tSN:C02HBa0190N21_LR41\tLN:10835\n-@SQ\tSN:C02HBa0190P16_LR331\tLN:10808\n-@SQ\tSN:C02HBa0194L19_LR42\tLN:10280\n-@SQ\tSN:C02HBa0204A09_LR332\tLN:10029\n-@SQ\tSN:C02HBa0204D01_LR334\tLN:9746\n-@SQ\tSN:C02HBa0214B22_LR325\tLN:9581\n-@SQ\tSN:C02HBa0215M12_LR319\tLN:9918\n-@SQ\tSN:C02HBa0228I09_LR329\tLN:10933\n-@SQ\tSN:C02HBa0236E02_LR326\tLN:9822\n-@SQ\tSN:C02HBa0284G15_LR47\tLN:9034\n-@SQ\tSN:C02HBa0291P19_LR48\tLN:9826\n-@SQ\tSN:C02HBa0329G05_LR52\tLN:9637\n-@SQ\tSN:C02SLe0010H16_LR53\tLN:10744\n-@SQ\tSN:C02SLe0018B07_LR335\tLN:9222\n-@SQ\tSN:C02SLe0034H10_LR327\tLN:10833\n-@SQ\tSN:C02SLe0127J16_LR59\tLN:10965\n-@SQ\tSN:C02SLe0132D01_LR60\tLN:10524\n-@SQ\tSN:C02SLm0057H03_LR336\tLN:9514\n-@SQ\tSN:C02SLm0057H03_LR64\tLN:9170\n-@SQ\tSN:C02SLm0057H03_LR65\tLN:9532\n-@SQ\tSN:C03HBa0012D06_LR72\tLN:10645\n-@SQ\tSN:C03HBa0030O03_LR74\tLN:10569\n-@SQ\tSN:C03HBa0034B23_LR76\tLN:10005\n-@SQ\tSN:C03HBa0040F22_LR77\tLN:10227\n-@SQ\tSN:C03HBa0054O21_LR78\tLN:9044\n-@SQ\tSN:C03HBa0076J13_LR79\tLN:10097\n-@SQ\tSN:C03HBa0233O20_LR82\tLN:9753\n-@SQ\tSN:C03HBa0295I12_LR83\tLN:10258\n-@SQ\tSN:C03HBa0318C22_LR84\tLN:10004\n-@SQ\tSN:C03HBa0323D22_LR85\tLN:9222\n-@SQ\tSN:C04HBa127N12_LR346\tLN:10533\n-@SQ\tSN:C04HBa132O11_LR104\tLN:10306\n-@SQ\tSN:C04HBa164O3_LR344\tLN:9345\n-@SQ\tSN:C04HBa190C13_LR106\tLN:10719\n-@SQ\tSN:C04HBa198I15_LR107\tLN:10673\n-@SQ\tSN:C04HBa219H8_LR109\tLN:10174\n-@SQ\tSN:C04HBa239P14_LR111\tLN:10483\n-@SQ\tSN:C04HBa255I2_LR112\tLN:10650\n-@SQ\tSN:C04HBa27G19_LR337\tLN:9788\n-@SQ\tSN:C04HBa2G1_LR120\tLN:9322\n-@SQ\tSN:C04HBa331L22_LR115\tLN:10697\n-@SQ\tSN:C04HBa35C16_LR339\tLN:9494\n-@SQ\tSN:C04HBa36C23_LR91\tLN:10103\n-@SQ\tSN:C04HBa50I18_LR341\tLN:10825\n-@SQ\tSN:C04HBa58E11_LR93\tLN:9927\n-@SQ\tSN:C04HBa66O12_LR94\tLN:9355\n-@SQ\tSN:C04HBa68N5_LR343\tLN:9886\n-@SQ\tSN:C04HBa6E18_LR87\tLN:9265\n-@SQ\tSN:C04HBa6O16_LR123\tLN:10386\n-@SQ\tSN:C04HBa78E4_LR98\tLN:9994\n-@SQ\tSN:C04HBa78J4_LR99\tLN:9165\n-@SQ\tSN:C04HBa80D3_LR100\tLN:9781\n-@SQ\tSN:C04HBa8K13_LR338\tLN:9345\n-@SQ\tSN:C04HBa96I8_LR101\tLN:9693\n-@SQ\tSN:C04SLm14G22_LR116\tLN:10306\n-@SQ\tSN:C04SLm39E17_LR117\tLN:9105\n-@SQ\tSN:C05HBa0003C20_LR126\tLN:9460\n-@SQ\tSN:C05HBa0006N20_LR128\tLN:1010'..b'i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09HBa0116C14_LR240,+6179,36M,0;\n-HWI-EAS337_3:7:1:1567:1795\t16\tC07HBa0309B15_LR190\t4202\t37\t36M\t*\t0\t0\tATAAACCCTAACACTTCTTCTCCTGTTACTGTTTCC\tUUUUMUVVWWVVVVWVVWVVWVWWWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:216:392\t0\tC04HBa96I8_LR101\t4961\t37\t36M\t*\t0\t0\tGAAGATTTTTTAATCTTGTGGTCTTAAACGTGTCAC\tWWWWWWWWWWWWWWWWWVWVUWWWWVVWWQUSUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:38:1803\t16\tC04HBa50I18_LR341\t2928\t37\t36M\t*\t0\t0\tCATACCTGATTTTTTGCCATATGTTTGTGATTTCAC\tUUUUUUWWWWWWWWWWWVWWWWWWWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:425:1196\t16\tC06HBa0217M17_LR166\t4141\t37\t36M\t*\t0\t0\tCAATCCTGCTTTAGCACTGCACTGTGATCTCTGCTC\tUUUUUUVVVVVWWVWWWVWWTVWWWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:181:410\t16\tC02HBa0072A04_LR26\t2348\t37\t36M\t*\t0\t0\tAAATCCTAATTACTTCCCCCCTCATTTCATTATTTC\tUUUUUUWWWVWWVWWWWVVVVWWWWVWVVWWWWWWV\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1065:1826\t16\tC09SLe0130H12_LR273\t4026\t0\t36M\t*\t0\t0\tTTATTCCCTGTCCATAGAAGGCATAAATAAGCAATC\tUUUUUUWVWWWVVWVWWWWVWVWWWWWWWWWWWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09HBa0116C14_LR240,+5410,36M,0;\n-HWI-EAS337_3:7:1:79:1444\t16\tC02HBa0027B01_LR21\t4337\t0\t36M\t*\t0\t0\tTCGGAAAGAAAACATCTAGAGCAGAGATCAATATTC\tRQUUUUWWWWWWVVWVVWWWWVWWWWWWWWWWWVWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C02SLe0018B07_LR335,+4851,36M,0;\n-HWI-EAS337_3:7:1:1634:1526\t16\tC09SLe0085A10_LR364\t607\t37\t36M\t*\t0\t0\tCCTTCTAGCAAAAGCCCTTCGAGTAGTCATATCTTC\tRRUUUUWVTWWWWVVVWWWVWWWWWWWVWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:462:1320\t16\tC12HBa326K10_LR306\t6488\t25\t36M\t*\t0\t0\tAAAGAAAAAAATAATAAATAATAATTAAATCAAAAC\tUUCUUUWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW\tXT:A:U\tNM:i:2\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:2C28G4\n-HWI-EAS337_3:7:1:532:1095\t0\tC04HBa50I18_LR341\t1\t37\t36M\t*\t0\t0\tGGTCTGGCTATTTGATTTCCACCTGCTACCCCCGCA\tWWWVWWWWWWVWWVVVWWVWWVVVTVVWVVUUUSUJ\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:27:305\t4\t*\t0\t0\t*\t*\t0\t0\tGATTGATTCAGTAATTGAGTTAACCTCTGAAAGAGA\tWWWVVWWWWWVWWWWVVWVWWWWWVWVWQVUUURRU\n-HWI-EAS337_3:7:1:832:1960\t16\tC07HBa0002M15_LR175\t7167\t0\t36M\t*\t0\t0\tCTTTGCCAAAACAAAGTGAAGTACTGGATGTACCTC\tPUUUUQKWWWWVWWWWWWWWWWWWWWWWWWWWWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:1\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09HBa0194K19_LR362,+1277,36M,0;C11HBa0029C01_LR281,-7887,36M,1;\n-HWI-EAS337_3:7:1:1312:645\t16\tC06HBa0120H21_LR161\t186\t37\t36M\t*\t0\t0\tTCAACTTTAGCTGCACCCTTGAATATGTGATTGTGC\tUQUUUUVVWWVWWVWVVVWWWWWWWWWWWWWWWVWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1107:226\t0\tC12HBa326K10_LR306\t5231\t37\t36M\t*\t0\t0\tGCAGAAAAAACGAATTTGTTTTGGCCCCCACTTCGT\tWWWWWWWWWWWWVVWWWVWWWWVQVVWWVVUUUURU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:274:1287\t0\tC09SLm0008K04_LR274\t10575\t37\t36M\t*\t0\t0\tGAGGATTTGCCTAGAGGTGCTTTTGTTTGTGAATAT\tWWWWWWWWWWWWWVVVVWWWWWWWVWWWVWRUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1772:270\t4\t*\t0\t0\t*\t*\t0\t0\tGGAAATACTAACTANANNNNNNNNNNNNNNNNNNNN\tWWVVWWWWWVWVWWCVCCCCCCCCCCCCCCCCCCC@\n-HWI-EAS337_3:7:1:1704:1373\t16\tC06HBa0217M17_LR166\t3360\t37\t36M\t*\t0\t0\tCAAACAATTCGAAGGTTTCCACAAATCAGCTTTACC\tQUUSSUWOVVWWWWWWWVVSWWWWSWWWVWWWWWWW\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:10A25\n-HWI-EAS337_3:7:1:241:903\t16\tC06HBa0066I09_LR156\t5444\t37\t36M\t*\t0\t0\tCATATTGAATTTGCTCATTCGACTTGGTACATTACC\tRUUUUUWVWWWWWWWVWWWVWWVWWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:404:1924\t16\tC08HBa0239G21_LR221\t4431\t37\t36M\t*\t0\t0\tGAGTGTTTGCAATCCAAGTGTTCGAGTTGCATCGAC\tUUUUUUWWWWVWWVWWWWWWWWWWWWWWWWWWWWWV\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:23:1455\t0\tC02HBa0190P16_LR331\t3279\t37\t36M\t*\t0\t0\tGGGGAATTGTTATGCTTTAAACTAATGGGAAAAGAA\tWWWWWWWWWWWWWVWVWWWVWVVWWWTVTWUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/part1.bam |
| b |
| Binary file SMART/data/part1.bam has changed |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/part1.sam --- a/SMART/data/part1.sam Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,448 +0,0 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:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:425:150\t16\tC02HBa0124N09_LR31\t1935\t37\t36M\t*\t0\t0\tTCCTCCAAGAAACTTCTCCGATTACTCTCCATTTGC\tRSUUSSWWVWWWWWWWWVVWWWWWWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:773:145\t16\tC04HBa164O3_LR344\t8533\t37\t36M\t*\t0\t0\tTTAGTATTGATTGTAAGGTGATCTGTTGGAAATTAC\tUUUUUUVWVVWWVVWWVWWVWWVVWWWWWWWWWWWW\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:4A31\n-HWI-EAS337_3:7:1:1191:747\t16\tC06HBa0147H20_LR146\t3868\t37\t36M\t*\t0\t0\tTGCGATAAAGAACAACTTCAATTGCAAAGTTAGATC\tKUUUUUWVWQWVVWVVVVVWWVWVVRWVWWWVWWVV\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:103:821\t4\t*\t0\t0\t*\t*\t0\t0\tGTAGAGGAGGTAGGCTTGGTGGTTCTGTAGATGTTT\tWWWWWWWWVWVWWVVWWUVVVVUVJWKVJKKURUUU\n-HWI-EAS337_3:7:1:1689:453\t0\tC09HBa0142I14_LR265\t8410\t37\t36M\t*\t0\t0\tGAAAAAAACACTCTGATTTGTAAGAGAGAATTTAAC\tWWWWWWWWWWWWWWWVWWVWVVVWWVWWVVUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:259:111\t16\tC09SLe0076N09_LR363\t6949\t0\t36M\t*\t0\t0\tATTCTGAGGACTATGCCTAGCAGCTGAAATCACCAC\tUUUUUUWVVVQVWVVVVWUWWVWWWWWWWWWWWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLm0143I09_LR365,-6949,36M,0;\n-HWI-EAS337_3:7:1:577:868\t16\tC12HBa149G24_LR381\t8433\t37\t36M\t*\t0\t0\tGTATGAAGAGGAGAAACTGCAAAAAGAAGCCTTAGC\tUUURUUVVWWWWWWWWVVVVWWWWWWWVWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1223:332\t16\tC04HBa27G19_LR337\t2599\t37\t36M\t*\t0\t0\tTTCCATGAAAACATTTTCCTTCATACCAAACACACC\tRRSRUUWWWWWVWWWWWVVWWVWWWVVWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1626:1930\t16\tC12HBa326K10_LR306\t9855\t37\t36M\t*\t0\t0\tGGATAAAGTTTGCGTATACACCACCCTTCCCATACC\tUUUUUUWVVVVWVVWWVWVWWWWWWWWWWWWWWVWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1310:342\t0\tC07HBa0287B22_LR188\t267\t25\t36M\t*\t0\t0\tGTTTATATGATCAGAAACGGATCCAGTTTCAGACAT\tWWWWWWWWVWWWWVWWWWTWWWWVWVVWWVURUUUU\tXT:A:U\tNM:i:2\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:12G4T18\n-HWI-EAS337_3:7:1:629:1071\t0\tC02SLm0057H03_LR65\t8840\t37\t36M\t*\t0\t0\tGAATCACCGTCGGTGCCGTCATCGGTGATGGTGGAC\tWWWWWWWWWWWWWVVWWVVWVVVWWVWDVTUMSUPC\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1306:1849\t16\tC04HBa8K13_LR338\t8095\t37\t36M\t*\t0\t0\tTTATTGAATCTGGGTTTGATCTCAAATCGAAGATAC\tUUUUUUWVVVVWWWWWWWWWVWVWWVWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1169:328\t0\tC04HBa164O3_LR344\t1860\t37\t36M\t*\t0\t0\tGATTGAATATCTCTCAACTAGAATAGACTCACCAAT\tWWWWWWWWWWWWWWVWWWWWVVWWWWVVWVUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:752:1933\t16\tC06HBa0106K23_LR159\t10004\t37\t36M\t*\t0\t0\tTGACAAACAGCAGCCAAAATACTACAGCCTGGAATC\t@CRQJUVQVOQWVVUWWWWWWWWVWWWWWWWWWWWW\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:4C31\n-HWI-EAS337_3:7:1:1726:1896\t0\tC09HBa0194K19_LR362\t423\t23\t36M\t*\t0\t0\tGTTCAAGGCTCGTTTAGTGGTTAAAGGATATTCACA\tWWWWWWVWWWWWVWWVWVWUVWVVWVTVWVUUSUUR\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:1\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C11HBa0029C01_LR281,-8741,36M,1;\n-HWI-EAS337_3:7:1:382:233\t16\tC04HBa80D3_LR100\t3451\t37\t36M\t*\t0\t0\tAATAAAGGCATCAAGAAGTATACAACCAAATTCTTC\tUUUUUUWWTWVVWWWWWWWWWVVWWVVWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1209:738\t16\tC09SLm0018L06_LR366\t5546\t37\t36M\t*\t0\t0\tTTTTCCAGACAAGCACGAAACTATATAAACCATTAC\tRUUUUSVVWJWWPVWVWWWWVWWWWVWWVVWWVWVW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/part2.bam |
| b |
| Binary file SMART/data/part2.bam has changed |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/part2.sam --- a/SMART/data/part2.sam Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,448 +0,0 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337_3:7:1:713:1296\t16\tC12SLeRI72J6_LR378\t4507\t37\t36M\t*\t0\t0\tTTGCCCACTATCTGTTATGTCCATGATTTTTCCTCC\tUUUUUUVWWWVWWWWWWWWWWWWWWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1703:1622\t16\tC05HBa0058L13_LR131\t135\t37\t36M\t*\t0\t0\tTAAGATCTTGAAAACTAAATGAAGCACTAAGAACAC\tUUUUUUKWWWWWWWLWWWWWWWWWVWVWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:114:374\t16\tC09HBa0113I06_LR360\t2601\t37\t36M\t*\t0\t0\tTCTGAATATGTATTTGCTTTTTTAGGGAAAAATAAC\tRSUUUUVWVVWWWWVVUVWWWWWWWWWWWWWWVWWW\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:32A3\n-HWI-EAS337_3:7:1:1688:1598\t0\tC04HBa80D3_LR100\t8540\t37\t36M\t*\t0\t0\tGACCGAAAGATGTCTAGTGGAAAGTAGCCCAGTGGA\tWWWWWWWWWWWWWWWWWWVVWWWWWWWWVWUUUSUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1164:1787\t4\t*\t0\t0\t*\t*\t0\t0\tGAAGTGTGAAATTGATAGATTTAGTGGGCGCACCAA\tWWWWWWWWWWVWWWWWWWWWWWWVVWVWVWUUUUUU\n-HWI-EAS337_3:7:1:321:1064\t16\tC05HBa0145P19_LR136\t7916\t37\t36M\t*\t0\t0\tACCATAAAACTGAGTCGTCAGAATGATTCTGCTTCC\tURUUUUWVWVVVWWWVWWWWWWWWWWWWWWWWVWVW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:168:1419\t0\tC07HBa0309B15_LR190\t1250\t0\t36M\t*\t0\t0\tGGATCTGTTGACCTTCCTAGGTCAAGACAAGTTTCA\tWWWWWWWWWVWWWWWWWWVVVWWWWVWWWWSUUUUU\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C04HBa255I2_LR112,+3312,36M,0;\n-HWI-EAS337_3:7:1:174:1900\t0\tC02HBa0167J21_LR39\t7262\t37\t36M\t*\t0\t0\tGAGGATGATCCATTAACCGCAGGAACAGTGGAGACT\tWWWWWWWWWWWWWWWVWWWWVWWWWWVWWWUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:399:1239\t16\tC04HBa35C16_LR339\t2042\t37\t36M\t*\t0\t0\tAAGCACATAACACTTCCACCATAAATGGACCATACC\tULSUUUWVWVVVWLVWVWVVWVWWWWVVWWWWWVWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:213:1008\t4\t*\t0\t0\t*\t*\t0\t0\tGATCTGTACACCTCTCTTTTTGCTGAATATATCAGC\tWWWWWWWWVWWWVWWWVVWVWVWWVVTWWWUUUURU\n-HWI-EAS337_3:7:1:656:1907\t16\tC05HBa0131D04_LR133\t767\t37\t36M\t*\t0\t0\tGAAGGTAATAGCATGATATATACCATGACAAGAATC\tUUUSUUWWVWVQWVVWVWWWVWVVWWWWVWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1622:793\t16\tC06HBa0120H21_LR161\t4515\t37\t36M\t*\t0\t0\tTGCTCAGATCCTCTTTCCTTTCTCCTAACCATAATC\tRUSUUUVWVWVVWVWWWVWWWVWVWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:736:1713\t4\t*\t0\t0\t*\t*\t0\t0\tGTAGAGGAGGTAGGCTTGGTGGTTCTGTAGATGTTT\tWWWWWWWWVWVVVWVWWQUUVVQVOWCVQQRUKUUU\n-HWI-EAS337_3:7:1:168:2006\t0\tC03HBa0012D06_LR72\t6920\t37\t36M\t*\t0\t0\tGCAGACCAAGCAAAATTATATTTATCTGGTATGGCT\tWWWWWWWWWWWWWWWULWWVWVWWWVTVQTUSSUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1707:99\t0\tC12HBa224N6_LR382\t6492\t37\t36M\t*\t0\t0\tGTAATGAGTAGATATGCAATTCAATGTCTTTCACTT\tWWWWWWWWWVWWWWWWWWWWWWVVWWVVVWUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:278:1921\t16\tC11SLm0052K14_LR376\t2794\t37\t36M\t*\t0\t0\tATGTGATAATGTCATCTGTATAAATGTTCTTAAAAC\tRUSUUUVWWVVVUWWWWWWWWVWWWWWWVWWWWVWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:307:1516\t16\tC11HBa0143O06_LR374\t6204\t37\t36M\t*\t0\t0\tAACAGTAGTATGCTGCATACCTTTTCAGTGGCAACC\tUUUUUUWWVWWWVWWVWWWVWVWWWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:489:749\t16\tC09SLm0143I09_LR365\t5492\t0\t36M\t*\t0\t0\tAACAATAGACCAGCAAAATATAGGATATCCAGAAAC\tUUJUURWVWKKWVQWWWWWWVWWWWWWVWWWWWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLe0076N09_LR363,-5492,36M,0;\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/part3.bam |
| b |
| Binary file SMART/data/part3.bam has changed |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/part3.sam --- a/SMART/data/part3.sam Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,448 +0,0 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WWWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:565:893\t16\tC09HBa0100J12_LR259\t5501\t0\t36M\t*\t0\t0\tAGCAGTTTGTTGGCTGCTGTTTTGAAGAGTGGAGTC\tUUUUUUWWWWVWVVWWWWWWWVWWWWWWWWWWWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLm0129J22_LR373,-5501,36M,0;\n-HWI-EAS337_3:7:1:1086:894\t0\tC07HBa0309F18_LR191\t6311\t37\t36M\t*\t0\t0\tGTGAAGCAGAAGATCTGCAATAACTCTTAAATTTGT\tWWWWWWWVWVVWWWWWWVVSVVVVWVVVVVUUUUSU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:904:892\t16\tC02HBa0016A12_LR19\t1326\t0\t36M\t*\t0\t0\tTGTGAAGAAAGAGGTCGTTTAAAAATCTGAAGTTCC\tUUUUUUWWWWWWWWWVWWWWWWWWWWWVWWWWWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C02HBa0236E02_LR326,+8462,36M,0;\n-HWI-EAS337_3:7:1:1201:1415\t0\tC06HBa0144J05_LR355\t1215\t0\t36M\t*\t0\t0\tGAGTTGGCAAAGTAGGAAGATCTCTTGAAGATTCAA\tWWWWWWWWWWVWWWWWWVWVWWWWWWVVWWUUUUUU\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C01HBa0003D15_LR7,+308,36M,0;\n-HWI-EAS337_3:7:1:157:1509\t0\tC05HBa0042B19_LR129\t1213\t37\t36M\t*\t0\t0\tGAATTAAGAAACGATTTCACTGAAGAACATAGAACT\tVVWWWVWVSWVVVVSVQHWQWWWQVVVQWWUUUUOS\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1150:1510\t16\tC04HBa164O3_LR344\t2069\t37\t36M\t*\t0\t0\tCCGACTAATGATATAATAAGGATGGTTTCATCTCCC\tRUSURUVWWWWWWVWVWWVWVWVVWWWWWWWWVWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:757:1140\t0\tC05HBa0138J03_LR135\t1491\t37\t36M\t*\t0\t0\tGAAAAAACTGAACTGATAAATGCCTACGAAAGATGT\tWWWWWWWWWWVWWWWWWWWWVWWWWVWVVVUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:397:1260\t16\tC04HBa239P14_LR111\t7648\t37\t36M\t*\t0\t0\tTGGCCAAGGATTGCAGATTAACTATAGTAAGAAAGC\tUUUSRUVVVVVWWWWWWWWWVWWWWWWWWVWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:370:525\t0\tC05HBa0135A02_LR134\t3139\t37\t36M\t*\t0\t0\tGTATAGGGTTTGAGCTAAAGTTGTTGACTTTAATTG\tWWWWWWWWWWWWWWWWWWWVWWVWWVWVWWUUUUUP\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:782:729\t0\tC04HBa35C16_LR339\t254\t37\t36M\t*\t0\t0\tGACTCTATCCGAAGGTGTTTTTTTGATGGATTAACC\tWWWWWWWWWWWWWWWVWWWWWWWWUVWQQVUUUSUR\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:31C4\n-HWI-EAS337_3:7:1:1602:38\t16\tC07HBa0002M15_LR175\t8458\t37\t36M\t*\t0\t0\tCTTCTGCTCTCTGTCCTTGTACAGGACAGACTCATC\tUURUSUWUVVVRVVVVVVVVVUWWVVWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:204:1509\t16\tC09SLe0068C01_LR272\t1470\t37\t36M\t*\t0\t0\tACTTTGTCACACTTAACCCTGTGAATCCTTGCTCTC\tUUUUUUVWWWWVVWWWWWWVWWWWWWWWWWWWWVWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1525:1263\t0\tC09SLe0085A10_LR364\t5595\t37\t36M\t*\t0\t0\tGGGTAAGAAGCATGTCACATCTATAAATATGAGGCT\tWWWWWWWWWWWWWWWWWWWWWWWWWVWWWWUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:895:1075\t16\tC09SLe0130H12_LR273\t8142\t0\t36M\t*\t0\t0\tTAGACATTTCTGCTCAATTTCGTTTTTTTGCTAGCC\tUUUUUUVVVWWWVWWWWWWWVWWWWWVWWWWWWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09HBa0116C14_LR240,+1294,36M,0;\n-HWI-EAS337_3:7:1:1204:1920\t16\tC07HBa0002D20_LR197\t3427\t37\t36M\t*\t0\t0\tTGGCTGTCTCCCCTTCTTTTATTCCAGGGGAAAAAC\tUUUUUUVVVVVWWWWVWWWWWWWVVWWWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:115:342\t0\tC06HBa0197N20_LR164\t5182\t37\t36M\t*\t0\t0\tGAATAACCTCCATAGTAGGCTTGAGAAATTGCTTTA\tWWWWWWWWVWVWWWWVVWWVWWWVWWWWWWUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/part4.bam |
| b |
| Binary file SMART/data/part4.bam has changed |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/part4.sam --- a/SMART/data/part4.sam Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,448 +0,0 @@\n-@SQ\tSN:C10HBa0111D09_LR276\tLN:9300\n-@SQ\tSN:C11HBa0029C01_LR281\tLN:10969\n-@SQ\tSN:C11HBa0034I10_LR282\tLN:9056\n-@SQ\tSN:C11HBa0054I23_LR283\tLN:10301\n-@SQ\tSN:C11HBa0062I24_LR284\tLN:10050\n-@SQ\tSN:C11HBa0064J13_LR285\tLN:9385\n-@SQ\tSN:C11HBa0072I13_LR286\tLN:9556\n-@SQ\tSN:C11HBa0089M02_LR287\tLN:9244\n-@SQ\tSN:C11HBa0096D22_LR288\tLN:9184\n-@SQ\tSN:C11HBa0107K14_LR289\tLN:9115\n-@SQ\tSN:C11HBa0139J14_LR291\tLN:10002\n-@SQ\tSN:C11HBa0143O06_LR374\tLN:10785\n-@SQ\tSN:C11HBa0161D01_LR292\tLN:9057\n-@SQ\tSN:C11HBa0168B23_LR293\tLN:9826\n-@SQ\tSN:C11HBa0190J03_LR294\tLN:10992\n-@SQ\tSN:C11HBa0249E07_LR279\tLN:10008\n-@SQ\tSN:C11HBa0303G16_LR296\tLN:9430\n-@SQ\tSN:C11HBa0323E19_LR297\tLN:9657\n-@SQ\tSN:C11SLe0053P22_LR298\tLN:9827\n-@SQ\tSN:C11SLm0052K14_LR376\tLN:10013\n-@SQ\tSN:C12HBa115G22_LR301\tLN:10021\n-@SQ\tSN:C12HBa120K4_LR313\tLN:10271\n-@SQ\tSN:C12HBa144B17_LR302\tLN:9247\n-@SQ\tSN:C12HBa149G24_LR381\tLN:9271\n-@SQ\tSN:C12HBa165B12_LR303\tLN:9257\n-@SQ\tSN:C12HBa183M6_LR379\tLN:9473\n-@SQ\tSN:C12HBa221M9_LR377\tLN:10755\n-@SQ\tSN:C12HBa224N6_LR382\tLN:9130\n-@SQ\tSN:C12HBa26C13_LR299\tLN:9139\n-@SQ\tSN:C12HBa326K10_LR306\tLN:10414\n-@SQ\tSN:C12HBa90D9_LR311\tLN:9638\n-@SQ\tSN:C12HBa93P12_LR312\tLN:9510\n-@SQ\tSN:C12SLe124D18_LR385\tLN:10545\n-@SQ\tSN:C12SLeRI72J6_LR378\tLN:9337\n-@SQ\tSN:C12SLm103K8_LR380\tLN:10118\n-@SQ\tSN:C01HBa0003D15_LR7\tLN:10776\n-@SQ\tSN:C01HBa0163B20_LR10\tLN:9321\n-@SQ\tSN:C01HBa0216G16_LR11\tLN:10332\n-@SQ\tSN:C01HBa0256E08_LR13\tLN:9024\n-@SQ\tSN:C01HBa0329A12_LR14\tLN:9536\n-@SQ\tSN:BAC19_LR16\tLN:9760\n-@SQ\tSN:C02HBa0008G02_LR67\tLN:9205\n-@SQ\tSN:C02HBa0011O23_LR68\tLN:9399\n-@SQ\tSN:C02HBa0016A12_LR19\tLN:9822\n-@SQ\tSN:C02HBa0027B01_LR21\tLN:9222\n-@SQ\tSN:C02HBa0030A21_LR22\tLN:9147\n-@SQ\tSN:C02HBa0046M08_LR23\tLN:10763\n-@SQ\tSN:C02HBa0072A04_LR26\tLN:9766\n-@SQ\tSN:C02HBa0075D08_LR28\tLN:10744\n-@SQ\tSN:C02HBa0124N09_LR31\tLN:9335\n-@SQ\tSN:C02HBa0155D20_LR36\tLN:10743\n-@SQ\tSN:C02HBa0155E05_LR37\tLN:10417\n-@SQ\tSN:C02HBa0164H08_LR38\tLN:10279\n-@SQ\tSN:C02HBa0167J21_LR39\tLN:9925\n-@SQ\tSN:C02HBa0185P07_LR40\tLN:9818\n-@SQ\tSN:C02HBa0190N21_LR41\tLN:10835\n-@SQ\tSN:C02HBa0190P16_LR331\tLN:10808\n-@SQ\tSN:C02HBa0194L19_LR42\tLN:10280\n-@SQ\tSN:C02HBa0204A09_LR332\tLN:10029\n-@SQ\tSN:C02HBa0204D01_LR334\tLN:9746\n-@SQ\tSN:C02HBa0214B22_LR325\tLN:9581\n-@SQ\tSN:C02HBa0215M12_LR319\tLN:9918\n-@SQ\tSN:C02HBa0228I09_LR329\tLN:10933\n-@SQ\tSN:C02HBa0236E02_LR326\tLN:9822\n-@SQ\tSN:C02HBa0284G15_LR47\tLN:9034\n-@SQ\tSN:C02HBa0291P19_LR48\tLN:9826\n-@SQ\tSN:C02HBa0329G05_LR52\tLN:9637\n-@SQ\tSN:C02SLe0010H16_LR53\tLN:10744\n-@SQ\tSN:C02SLe0018B07_LR335\tLN:9222\n-@SQ\tSN:C02SLe0034H10_LR327\tLN:10833\n-@SQ\tSN:C02SLe0127J16_LR59\tLN:10965\n-@SQ\tSN:C02SLe0132D01_LR60\tLN:10524\n-@SQ\tSN:C02SLm0057H03_LR336\tLN:9514\n-@SQ\tSN:C02SLm0057H03_LR64\tLN:9170\n-@SQ\tSN:C02SLm0057H03_LR65\tLN:9532\n-@SQ\tSN:C03HBa0012D06_LR72\tLN:10645\n-@SQ\tSN:C03HBa0030O03_LR74\tLN:10569\n-@SQ\tSN:C03HBa0034B23_LR76\tLN:10005\n-@SQ\tSN:C03HBa0040F22_LR77\tLN:10227\n-@SQ\tSN:C03HBa0054O21_LR78\tLN:9044\n-@SQ\tSN:C03HBa0076J13_LR79\tLN:10097\n-@SQ\tSN:C03HBa0233O20_LR82\tLN:9753\n-@SQ\tSN:C03HBa0295I12_LR83\tLN:10258\n-@SQ\tSN:C03HBa0318C22_LR84\tLN:10004\n-@SQ\tSN:C03HBa0323D22_LR85\tLN:9222\n-@SQ\tSN:C04HBa127N12_LR346\tLN:10533\n-@SQ\tSN:C04HBa132O11_LR104\tLN:10306\n-@SQ\tSN:C04HBa164O3_LR344\tLN:9345\n-@SQ\tSN:C04HBa190C13_LR106\tLN:10719\n-@SQ\tSN:C04HBa198I15_LR107\tLN:10673\n-@SQ\tSN:C04HBa219H8_LR109\tLN:10174\n-@SQ\tSN:C04HBa239P14_LR111\tLN:10483\n-@SQ\tSN:C04HBa255I2_LR112\tLN:10650\n-@SQ\tSN:C04HBa27G19_LR337\tLN:9788\n-@SQ\tSN:C04HBa2G1_LR120\tLN:9322\n-@SQ\tSN:C04HBa331L22_LR115\tLN:10697\n-@SQ\tSN:C04HBa35C16_LR339\tLN:9494\n-@SQ\tSN:C04HBa36C23_LR91\tLN:10103\n-@SQ\tSN:C04HBa50I18_LR341\tLN:10825\n-@SQ\tSN:C04HBa58E11_LR93\tLN:9927\n-@SQ\tSN:C04HBa66O12_LR94\tLN:9355\n-@SQ\tSN:C04HBa68N5_LR343\tLN:9886\n-@SQ\tSN:C04HBa6E18_LR87\tLN:9265\n-@SQ\tSN:C04HBa6O16_LR123\tLN:10386\n-@SQ\tSN:C04HBa78E4_LR98\tLN:9994\n-@SQ\tSN:C04HBa78J4_LR99\tLN:9165\n-@SQ\tSN:C04HBa80D3_LR100\tLN:9781\n-@SQ\tSN:C04HBa8K13_LR338\tLN:9345\n-@SQ\tSN:C04HBa96I8_LR101\tLN:9693\n-@SQ\tSN:C04SLm14G22_LR116\tLN:10306\n-@SQ\tSN:C04SLm39E17_LR117\tLN:9105\n-@SQ\tSN:C05HBa0003C20_LR126\tLN:9460\n-@SQ\tSN:C05HBa0006N20_LR128\tLN:1010'..b'\t*\t0\t0\tCTTATTTCTCATGCAACTTTTTTTTTGAAAAGTTTC\tRUUUUSWWVWWWWWWVWWWWWWWVWWWWWWWWWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLm0143I09_LR365,-9770,36M,0;\n-HWI-EAS337_3:7:1:5:1770\t0\tC02HBa0185P07_LR40\t1386\t37\t36M\t*\t0\t0\tGTGTGAAAAAGTATTTCATTCACATATTGAGTTGTT\tWWWWWWWWWWVWWWWWWWWWWWWWWWWWVVSUUQUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:115:1005\t0\tC11HBa0161D01_LR292\t3394\t37\t36M\t*\t0\t0\tGATTTTACTGGAATGGGGAAGGGTGAGGCATGGGTG\tWWWWWWWWWVVWWWVVVVWWVVVWWWVVWVUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:354:1708\t0\tC09HBa0165P17_LR241\t4985\t37\t36M\t*\t0\t0\tGCATCCGACAGTGACTTAGACGATGAGGAATACGAG\tWWWWWWWWWWWWVWWWWWVWWVWWVWWVWWUUUUUR\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1639:1500\t0\tC11SLm0052K14_LR376\t2483\t37\t36M\t*\t0\t0\tGTGATTATTATCTAACTCTGCAACAGCATCCAGGGA\tWWWWWWVVWWWWWVVWVVWUVVVVVVVVWVUUUUUR\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:766:243\t16\tC07HBa0308M01_LR189\t6701\t37\t36M\t*\t0\t0\tAGCAACAATCTCCAATTTATCTTCCATAGATGCCAC\tUSJUURWWVTVVVWWWWWWWVWWVVWWWWWWWWVWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:920:144\t0\tC05HBa0138J03_LR135\t8153\t37\t36M\t*\t0\t0\tGTGCGATCACACTGTTTATGTTGTTGTTGATCATTG\tWWVVWWWWWVWPWVWWVWWSWVSWWHWWLVUCPUUH\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:389:268\t16\tC12SLeRI72J6_LR378\t6610\t37\t36M\t*\t0\t0\tAAATTCTTTGAGGGTGGTTGCCCTCTCTAATTGACC\tUUUUUSVVWWWWWWWWWWWWVVWWWWVWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:294:1868\t0\tC04HBa58E11_LR93\t7287\t25\t36M\t*\t0\t0\tGAAAAAAAATTGTTTGTCTTGAATTAATGTTTCAAT\tVWVWWWWWWWWVQWWWWOWVVWWVWVVWQWUURULU\tXT:A:U\tNM:i:2\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:0T0G34\n-HWI-EAS337_3:7:1:1147:62\t0\tC02HBa0204D01_LR334\t6554\t37\t36M\t*\t0\t0\tGAATTCCCCTCAGGTTGGAGTTGTGCACTTGGCACT\tWWWWWWWWWWWWVWWWWWWVWWVWVVWVVWUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:787:1759\t16\tC02SLe0018B07_LR335\t8378\t0\t36M\t*\t0\t0\tCAGAAAATCAGAACAGCTACCAATTCTAATAAAACC\tHUUUUUVVTVVWVUWWUWWUVWWWWWWWVWWWWVVW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C02HBa0027B01_LR21,+810,36M,0;\n-HWI-EAS337_3:7:1:425:1939\t16\tC09SLe0076N09_LR363\t1546\t0\t36M\t*\t0\t0\tAAGTTTAGCCACATAGACCCAGACACCACAATTAGC\tUUUUUUWVVVWVVWWWVVVVWWWVWWWWVWWVWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLm0143I09_LR365,-1546,36M,0;\n-HWI-EAS337_3:7:1:187:1132\t0\tC02HBa0027B01_LR21\t10\t0\t36M\t*\t0\t0\tGTGGGAGAGGCAAGGGGCTTGGCTCATATCCTCTTC\tWVWWWWWWWWWWWWWWWWWWWTVWVWWWVVUUUUUU\tXT:A:R\tNM:i:1\tX0:i:2\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:21T14\tXA:Z:C02SLe0018B07_LR335,-9178,36M,1;\n-HWI-EAS337_3:7:1:1739:1840\t0\tC02HBa0072A04_LR26\t2868\t37\t36M\t*\t0\t0\tGGAGGGGTGAAATCGTTTCTGAAAAATAATGAAATG\tWWVWWWWWWWWWWWWWWVTWWWVVVWWWWWUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1505:1876\t0\tC07SLe0111B06_LR194\t8673\t37\t36M\t*\t0\t0\tGAAAGATCAAGTGTTGTCAAGTTCACTAGTTTAGAG\tWWWWWWWWWWWWWWWWWWWWVWWVWWWVVVUUUSUR\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:447:192\t0\tC09SLm0143I09_LR365\t6957\t0\t36M\t*\t0\t0\tGACTATGCCTAGCAGCTGAAATCACCACAACAAGTT\tWWWWWWWWWWWWWWWTWWWVVWWVWWWWWVUUUUUU\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLe0076N09_LR363,+6957,36M,0;\n-HWI-EAS337_3:7:1:21:2019\t16\tC09SLm0037I08_LR367\t1298\t37\t36M\t*\t0\t0\tGGGCTGGAAGACAGGTTATCATCTTTTACCTCATAC\tUUURUUWWWVVQWWWWWWWWWWWWWWWVVWWVVWWV\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1593:652\t0\tC04HBa8K13_LR338\t2175\t37\t36M\t*\t0\t0\tGTGATGAGTAAAACATCATCATATGAACTTGAAGAG\tWWWVWVWWVWVWWVWWWWWWVVWWVWWVWWUUUSUU\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:28A7\n-HWI-EAS337_3:7:1:1254:1660\t0\tC12HBa326K10_LR306\t8100\t37\t36M\t*\t0\t0\tGAAGTTTGTAATTCCTTTTAGGATTGTGGTTAACAT\tWWWVVWWWWWWWWWWWVWVWVUWWWTWVQWUUUUMU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:291:629\t4\t*\t0\t0\t*\t*\t0\t0\tGTAGAGGAGGTAGGCTTGGTGGTCCCTCTATGGTAA\tWWWWWWWWWWVVVWVWVVWTWWKOVVTRVSUSSMFR\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/samFile.sam --- a/SMART/data/samFile.sam Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1448 +0,0 @@\n-@SQ\tSN:C10HBa0111D09_LR276\tLN:9300\n-@SQ\tSN:C11HBa0029C01_LR281\tLN:10969\n-@SQ\tSN:C11HBa0034I10_LR282\tLN:9056\n-@SQ\tSN:C11HBa0054I23_LR283\tLN:10301\n-@SQ\tSN:C11HBa0062I24_LR284\tLN:10050\n-@SQ\tSN:C11HBa0064J13_LR285\tLN:9385\n-@SQ\tSN:C11HBa0072I13_LR286\tLN:9556\n-@SQ\tSN:C11HBa0089M02_LR287\tLN:9244\n-@SQ\tSN:C11HBa0096D22_LR288\tLN:9184\n-@SQ\tSN:C11HBa0107K14_LR289\tLN:9115\n-@SQ\tSN:C11HBa0139J14_LR291\tLN:10002\n-@SQ\tSN:C11HBa0143O06_LR374\tLN:10785\n-@SQ\tSN:C11HBa0161D01_LR292\tLN:9057\n-@SQ\tSN:C11HBa0168B23_LR293\tLN:9826\n-@SQ\tSN:C11HBa0190J03_LR294\tLN:10992\n-@SQ\tSN:C11HBa0249E07_LR279\tLN:10008\n-@SQ\tSN:C11HBa0303G16_LR296\tLN:9430\n-@SQ\tSN:C11HBa0323E19_LR297\tLN:9657\n-@SQ\tSN:C11SLe0053P22_LR298\tLN:9827\n-@SQ\tSN:C11SLm0052K14_LR376\tLN:10013\n-@SQ\tSN:C12HBa115G22_LR301\tLN:10021\n-@SQ\tSN:C12HBa120K4_LR313\tLN:10271\n-@SQ\tSN:C12HBa144B17_LR302\tLN:9247\n-@SQ\tSN:C12HBa149G24_LR381\tLN:9271\n-@SQ\tSN:C12HBa165B12_LR303\tLN:9257\n-@SQ\tSN:C12HBa183M6_LR379\tLN:9473\n-@SQ\tSN:C12HBa221M9_LR377\tLN:10755\n-@SQ\tSN:C12HBa224N6_LR382\tLN:9130\n-@SQ\tSN:C12HBa26C13_LR299\tLN:9139\n-@SQ\tSN:C12HBa326K10_LR306\tLN:10414\n-@SQ\tSN:C12HBa90D9_LR311\tLN:9638\n-@SQ\tSN:C12HBa93P12_LR312\tLN:9510\n-@SQ\tSN:C12SLe124D18_LR385\tLN:10545\n-@SQ\tSN:C12SLeRI72J6_LR378\tLN:9337\n-@SQ\tSN:C12SLm103K8_LR380\tLN:10118\n-@SQ\tSN:C01HBa0003D15_LR7\tLN:10776\n-@SQ\tSN:C01HBa0163B20_LR10\tLN:9321\n-@SQ\tSN:C01HBa0216G16_LR11\tLN:10332\n-@SQ\tSN:C01HBa0256E08_LR13\tLN:9024\n-@SQ\tSN:C01HBa0329A12_LR14\tLN:9536\n-@SQ\tSN:BAC19_LR16\tLN:9760\n-@SQ\tSN:C02HBa0008G02_LR67\tLN:9205\n-@SQ\tSN:C02HBa0011O23_LR68\tLN:9399\n-@SQ\tSN:C02HBa0016A12_LR19\tLN:9822\n-@SQ\tSN:C02HBa0027B01_LR21\tLN:9222\n-@SQ\tSN:C02HBa0030A21_LR22\tLN:9147\n-@SQ\tSN:C02HBa0046M08_LR23\tLN:10763\n-@SQ\tSN:C02HBa0072A04_LR26\tLN:9766\n-@SQ\tSN:C02HBa0075D08_LR28\tLN:10744\n-@SQ\tSN:C02HBa0124N09_LR31\tLN:9335\n-@SQ\tSN:C02HBa0155D20_LR36\tLN:10743\n-@SQ\tSN:C02HBa0155E05_LR37\tLN:10417\n-@SQ\tSN:C02HBa0164H08_LR38\tLN:10279\n-@SQ\tSN:C02HBa0167J21_LR39\tLN:9925\n-@SQ\tSN:C02HBa0185P07_LR40\tLN:9818\n-@SQ\tSN:C02HBa0190N21_LR41\tLN:10835\n-@SQ\tSN:C02HBa0190P16_LR331\tLN:10808\n-@SQ\tSN:C02HBa0194L19_LR42\tLN:10280\n-@SQ\tSN:C02HBa0204A09_LR332\tLN:10029\n-@SQ\tSN:C02HBa0204D01_LR334\tLN:9746\n-@SQ\tSN:C02HBa0214B22_LR325\tLN:9581\n-@SQ\tSN:C02HBa0215M12_LR319\tLN:9918\n-@SQ\tSN:C02HBa0228I09_LR329\tLN:10933\n-@SQ\tSN:C02HBa0236E02_LR326\tLN:9822\n-@SQ\tSN:C02HBa0284G15_LR47\tLN:9034\n-@SQ\tSN:C02HBa0291P19_LR48\tLN:9826\n-@SQ\tSN:C02HBa0329G05_LR52\tLN:9637\n-@SQ\tSN:C02SLe0010H16_LR53\tLN:10744\n-@SQ\tSN:C02SLe0018B07_LR335\tLN:9222\n-@SQ\tSN:C02SLe0034H10_LR327\tLN:10833\n-@SQ\tSN:C02SLe0127J16_LR59\tLN:10965\n-@SQ\tSN:C02SLe0132D01_LR60\tLN:10524\n-@SQ\tSN:C02SLm0057H03_LR336\tLN:9514\n-@SQ\tSN:C02SLm0057H03_LR64\tLN:9170\n-@SQ\tSN:C02SLm0057H03_LR65\tLN:9532\n-@SQ\tSN:C03HBa0012D06_LR72\tLN:10645\n-@SQ\tSN:C03HBa0030O03_LR74\tLN:10569\n-@SQ\tSN:C03HBa0034B23_LR76\tLN:10005\n-@SQ\tSN:C03HBa0040F22_LR77\tLN:10227\n-@SQ\tSN:C03HBa0054O21_LR78\tLN:9044\n-@SQ\tSN:C03HBa0076J13_LR79\tLN:10097\n-@SQ\tSN:C03HBa0233O20_LR82\tLN:9753\n-@SQ\tSN:C03HBa0295I12_LR83\tLN:10258\n-@SQ\tSN:C03HBa0318C22_LR84\tLN:10004\n-@SQ\tSN:C03HBa0323D22_LR85\tLN:9222\n-@SQ\tSN:C04HBa127N12_LR346\tLN:10533\n-@SQ\tSN:C04HBa132O11_LR104\tLN:10306\n-@SQ\tSN:C04HBa164O3_LR344\tLN:9345\n-@SQ\tSN:C04HBa190C13_LR106\tLN:10719\n-@SQ\tSN:C04HBa198I15_LR107\tLN:10673\n-@SQ\tSN:C04HBa219H8_LR109\tLN:10174\n-@SQ\tSN:C04HBa239P14_LR111\tLN:10483\n-@SQ\tSN:C04HBa255I2_LR112\tLN:10650\n-@SQ\tSN:C04HBa27G19_LR337\tLN:9788\n-@SQ\tSN:C04HBa2G1_LR120\tLN:9322\n-@SQ\tSN:C04HBa331L22_LR115\tLN:10697\n-@SQ\tSN:C04HBa35C16_LR339\tLN:9494\n-@SQ\tSN:C04HBa36C23_LR91\tLN:10103\n-@SQ\tSN:C04HBa50I18_LR341\tLN:10825\n-@SQ\tSN:C04HBa58E11_LR93\tLN:9927\n-@SQ\tSN:C04HBa66O12_LR94\tLN:9355\n-@SQ\tSN:C04HBa68N5_LR343\tLN:9886\n-@SQ\tSN:C04HBa6E18_LR87\tLN:9265\n-@SQ\tSN:C04HBa6O16_LR123\tLN:10386\n-@SQ\tSN:C04HBa78E4_LR98\tLN:9994\n-@SQ\tSN:C04HBa78J4_LR99\tLN:9165\n-@SQ\tSN:C04HBa80D3_LR100\tLN:9781\n-@SQ\tSN:C04HBa8K13_LR338\tLN:9345\n-@SQ\tSN:C04HBa96I8_LR101\tLN:9693\n-@SQ\tSN:C04SLm14G22_LR116\tLN:10306\n-@SQ\tSN:C04SLm39E17_LR117\tLN:9105\n-@SQ\tSN:C05HBa0003C20_LR126\tLN:9460\n-@SQ\tSN:C05HBa0006N20_LR128\tLN:101'..b'\t*\t0\t0\tCTTATTTCTCATGCAACTTTTTTTTTGAAAAGTTTC\tRUUUUSWWVWWWWWWVWWWWWWWVWWWWWWWWWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLm0143I09_LR365,-9770,36M,0;\n-HWI-EAS337_3:7:1:5:1770\t0\tC02HBa0185P07_LR40\t1386\t37\t36M\t*\t0\t0\tGTGTGAAAAAGTATTTCATTCACATATTGAGTTGTT\tWWWWWWWWWWVWWWWWWWWWWWWWWWWWVVSUUQUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:115:1005\t0\tC11HBa0161D01_LR292\t3394\t37\t36M\t*\t0\t0\tGATTTTACTGGAATGGGGAAGGGTGAGGCATGGGTG\tWWWWWWWWWVVWWWVVVVWWVVVWWWVVWVUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:354:1708\t0\tC09HBa0165P17_LR241\t4985\t37\t36M\t*\t0\t0\tGCATCCGACAGTGACTTAGACGATGAGGAATACGAG\tWWWWWWWWWWWWVWWWWWVWWVWWVWWVWWUUUUUR\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1639:1500\t0\tC11SLm0052K14_LR376\t2483\t37\t36M\t*\t0\t0\tGTGATTATTATCTAACTCTGCAACAGCATCCAGGGA\tWWWWWWVVWWWWWVVWVVWUVVVVVVVVWVUUUUUR\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:766:243\t16\tC07HBa0308M01_LR189\t6701\t37\t36M\t*\t0\t0\tAGCAACAATCTCCAATTTATCTTCCATAGATGCCAC\tUSJUURWWVTVVVWWWWWWWVWWVVWWWWWWWWVWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:920:144\t0\tC05HBa0138J03_LR135\t8153\t37\t36M\t*\t0\t0\tGTGCGATCACACTGTTTATGTTGTTGTTGATCATTG\tWWVVWWWWWVWPWVWWVWWSWVSWWHWWLVUCPUUH\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:389:268\t16\tC12SLeRI72J6_LR378\t6610\t37\t36M\t*\t0\t0\tAAATTCTTTGAGGGTGGTTGCCCTCTCTAATTGACC\tUUUUUSVVWWWWWWWWWWWWVVWWWWVWWWWWWWWW\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:294:1868\t0\tC04HBa58E11_LR93\t7287\t25\t36M\t*\t0\t0\tGAAAAAAAATTGTTTGTCTTGAATTAATGTTTCAAT\tVWVWWWWWWWWVQWWWWOWVVWWVWVVWQWUURULU\tXT:A:U\tNM:i:2\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:0T0G34\n-HWI-EAS337_3:7:1:1147:62\t0\tC02HBa0204D01_LR334\t6554\t37\t36M\t*\t0\t0\tGAATTCCCCTCAGGTTGGAGTTGTGCACTTGGCACT\tWWWWWWWWWWWWVWWWWWWVWWVWVVWVVWUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:787:1759\t16\tC02SLe0018B07_LR335\t8378\t0\t36M\t*\t0\t0\tCAGAAAATCAGAACAGCTACCAATTCTAATAAAACC\tHUUUUUVVTVVWVUWWUWWUVWWWWWWWVWWWWVVW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C02HBa0027B01_LR21,+810,36M,0;\n-HWI-EAS337_3:7:1:425:1939\t16\tC09SLe0076N09_LR363\t1546\t0\t36M\t*\t0\t0\tAAGTTTAGCCACATAGACCCAGACACCACAATTAGC\tUUUUUUWVVVWVVWWWVVVVWWWVWWWWVWWVWWWW\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLm0143I09_LR365,-1546,36M,0;\n-HWI-EAS337_3:7:1:187:1132\t0\tC02HBa0027B01_LR21\t10\t0\t36M\t*\t0\t0\tGTGGGAGAGGCAAGGGGCTTGGCTCATATCCTCTTC\tWVWWWWWWWWWWWWWWWWWWWTVWVWWWVVUUUUUU\tXT:A:R\tNM:i:1\tX0:i:2\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:21T14\tXA:Z:C02SLe0018B07_LR335,-9178,36M,1;\n-HWI-EAS337_3:7:1:1739:1840\t0\tC02HBa0072A04_LR26\t2868\t37\t36M\t*\t0\t0\tGGAGGGGTGAAATCGTTTCTGAAAAATAATGAAATG\tWWVWWWWWWWWWWWWWWVTWWWVVVWWWWWUUUUUU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1505:1876\t0\tC07SLe0111B06_LR194\t8673\t37\t36M\t*\t0\t0\tGAAAGATCAAGTGTTGTCAAGTTCACTAGTTTAGAG\tWWWWWWWWWWWWWWWWWWWWVWWVWWWVVVUUUSUR\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:447:192\t0\tC09SLm0143I09_LR365\t6957\t0\t36M\t*\t0\t0\tGACTATGCCTAGCAGCTGAAATCACCACAACAAGTT\tWWWWWWWWWWWWWWWTWWWVVWWVWWWWWVUUUUUU\tXT:A:R\tNM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLe0076N09_LR363,+6957,36M,0;\n-HWI-EAS337_3:7:1:21:2019\t16\tC09SLm0037I08_LR367\t1298\t37\t36M\t*\t0\t0\tGGGCTGGAAGACAGGTTATCATCTTTTACCTCATAC\tUUURUUWWWVVQWWWWWWWWWWWWWWWVVWWVVWWV\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1593:652\t0\tC04HBa8K13_LR338\t2175\t37\t36M\t*\t0\t0\tGTGATGAGTAAAACATCATCATATGAACTTGAAGAG\tWWWVWVWWVWVWWVWWWWWWVVWWVWWVWWUUUSUU\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:28A7\n-HWI-EAS337_3:7:1:1254:1660\t0\tC12HBa326K10_LR306\t8100\t37\t36M\t*\t0\t0\tGAAGTTTGTAATTCCTTTTAGGATTGTGGTTAACAT\tWWWVVWWWWWWWWWWWVWVWVUWWWTWVQWUUUUMU\tXT:A:U\tNM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:291:629\t4\t*\t0\t0\t*\t*\t0\t0\tGTAGAGGAGGTAGGCTTGGTGGTCCCTCTATGGTAA\tWWWWWWWWWWVVVWVWVVWTWWKOVVTRVSUSSMFR\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/sortedBamFile.bam |
| b |
| Binary file SMART/data/sortedBamFile.bam has changed |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/test.gff.gff3 --- a/SMART/data/test.gff.gff3 Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,218 +0,0 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lf);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:216:392;identity=100\n-C04HBa50I18_LR341\tSMART\ttranscript\t2928\t2963\t36\t-\t.\tName=HWI-EAS337_3:7:1:38:1803;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:38:1803;identity=100\n-C06HBa0217M17_LR166\tSMART\ttranscript\t4141\t4176\t36\t-\t.\tName=HWI-EAS337_3:7:1:425:1196;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:425:1196;identity=100\n-C02HBa0072A04_LR26\tSMART\ttranscript\t2348\t2383\t36\t-\t.\tName=HWI-EAS337_3:7:1:181:410;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:181:410;identity=100\n-C09SLe0130H12_LR273\tSMART\ttranscript\t4026\t4061\t36\t-\t.\tName=HWI-EAS337_3:7:1:1065:1826;quality=0;bestRegion=(self);nbGaps=0;nbOccurrences=2;nbMismatches=0;ID=HWI-EAS337_3:7:1:1065:1826;identity=100\n-C02HBa0027B01_LR21\tSMART\ttranscript\t4337\t4372\t36\t-\t.\tName=HWI-EAS337_3:7:1:79:1444;quality=0;bestRegion=(self);nbGaps=0;nbOccurrences=2;nbMismatches=0;ID=HWI-EAS337_3:7:1:79:1444;identity=100\n-C09SLe0085A10_LR364\tSMART\ttranscript\t607\t642\t36\t-\t.\tName=HWI-EAS337_3:7:1:1634:1526;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:1634:1526;identity=100\n-C12HBa326K10_LR306\tSMART\ttranscript\t6488\t6523\t36\t-\t.\tName=HWI-EAS337_3:7:1:462:1320;quality=25;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=2;ID=HWI-EAS337_3:7:1:462:1320;identity=94\n-C04HBa50I18_LR341\tSMART\ttranscript\t1\t36\t36\t+\t.\tName=HWI-EAS337_3:7:1:532:1095;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:532:1095;identity=100\n-C07HBa0002M15_LR175\tSMART\ttranscript\t7167\t7202\t36\t-\t.\tName=HWI-EAS337_3:7:1:832:1960;quality=0;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=0;ID=HWI-EAS337_3:7:1:832:1960;identity=100\n-C06HBa0120H21_LR161\tSMART\ttranscript\t186\t221\t36\t-\t.\tName=HWI-EAS337_3:7:1:1312:645;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:1312:645;identity=100\n-C12HBa326K10_LR306\tSMART\ttranscript\t5231\t5266\t36\t+\t.\tName=HWI-EAS337_3:7:1:1107:226;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:1107:226;identity=100\n-C09SLm0008K04_LR274\tSMART\ttranscript\t10575\t10610\t36\t+\t.\tName=HWI-EAS337_3:7:1:274:1287;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:274:1287;identity=100\n-C06HBa0217M17_LR166\tSMART\ttranscript\t3360\t3395\t36\t-\t.\tName=HWI-EAS337_3:7:1:1704:1373;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=HWI-EAS337_3:7:1:1704:1373;identity=97\n-C06HBa0066I09_LR156\tSMART\ttranscript\t5444\t5479\t36\t-\t.\tName=HWI-EAS337_3:7:1:241:903;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:241:903;identity=100\n-C08HBa0239G21_LR221\tSMART\ttranscript\t4431\t4466\t36\t-\t.\tName=HWI-EAS337_3:7:1:404:1924;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:404:1924;identity=100\n-C02HBa0190P16_LR331\tSMART\ttranscript\t3279\t3314\t36\t+\t.\tName=HWI-EAS337_3:7:1:23:1455;quality=37;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=HWI-EAS337_3:7:1:23:1455;identity=100\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/test_clusterize.gff3 --- a/SMART/data/test_clusterize.gff3 Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,213 +0,0 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HWI-EAS337_3:7:1:647:1863;identity=100\n-C02SLe0018B07_LR335\tS-MART\ttranscript\t8723\t8758\t36\t-\t.\tName=HWI-EAS337_3:7:1:1633:1841;nbMismatches=0;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=2;quality=0;ID=HWI-EAS337_3:7:1:1633:1841;identity=100\n-C02HBa0155E05_LR37\tS-MART\ttranscript\t4273\t4308\t36\t-\t.\tName=HWI-EAS337_3:7:1:34:1851;nbMismatches=1;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=2;quality=23;ID=HWI-EAS337_3:7:1:34:1851;identity=97\n-C08SLm0118A18_LR226\tS-MART\ttranscript\t4396\t4431\t36\t+\t.\tName=HWI-EAS337_3:7:1:600:1107;nbMismatches=0;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=1;quality=37;ID=HWI-EAS337_3:7:1:600:1107;identity=100\n-C02HBa0027B01_LR21\tS-MART\ttranscript\t1887\t1922\t36\t+\t.\tName=HWI-EAS337_3:7:1:1545:1519;nbMismatches=1;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=2;quality=0;ID=HWI-EAS337_3:7:1:1545:1519;identity=97\n-C02HBa0027B01_LR21\tS-MART\ttranscript\t4337\t4372\t36\t-\t.\tName=HWI-EAS337_3:7:1:79:1444;nbMismatches=0;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=2;quality=0;ID=HWI-EAS337_3:7:1:79:1444;identity=100\n-C02HBa0027B01_LR21\tS-MART\ttranscript\t5114\t5149\t36\t-\t.\tName=HWI-EAS337_3:7:1:1177:1504;nbMismatches=0;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=2;quality=0;ID=HWI-EAS337_3:7:1:1177:1504;identity=100\n-C02HBa0027B01_LR21\tS-MART\ttranscript\t5948\t5983\t36\t-\t.\tName=HWI-EAS337_3:7:1:31:1659;nbMismatches=0;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=2;quality=0;ID=HWI-EAS337_3:7:1:31:1659;identity=100\n-C07SLe0111B06_LR194\tS-MART\ttranscript\t8883\t8918\t36\t+\t.\tName=HWI-EAS337_3:7:1:1477:1673;nbMismatches=0;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=1;quality=37;ID=HWI-EAS337_3:7:1:1477:1673;identity=100\n-C02HBa0072A04_LR26\tS-MART\ttranscript\t932\t967\t36\t-\t.\tName=HWI-EAS337_3:7:1:141:1433;nbMismatches=0;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=1;quality=37;ID=HWI-EAS337_3:7:1:141:1433;identity=100\n-C02HBa0072A04_LR26\tS-MART\ttranscript\t2303\t2338\t36\t-\t.\tName=HWI-EAS337_3:7:1:1254:1491;nbMismatches=0;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=1;quality=37;ID=HWI-EAS337_3:7:1:1254:1491;identity=100\n-C02HBa0072A04_LR26\tS-MART\ttranscript\t2348\t2383\t36\t-\t.\tName=HWI-EAS337_3:7:1:181:410;nbMismatches=0;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=1;quality=37;ID=HWI-EAS337_3:7:1:181:410;identity=100\n-C02HBa0072A04_LR26\tS-MART\ttranscript\t6848\t6883\t36\t-\t.\tName=HWI-EAS337_3:7:1:373:2009;nbMismatches=1;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=1;quality=37;ID=HWI-EAS337_3:7:1:373:2009;identity=97\n-C08HBa0165B06_LR218\tS-MART\ttranscript\t3619\t3654\t36\t-\t.\tName=HWI-EAS337_3:7:1:447:1231;nbMismatches=0;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=1;quality=37;ID=HWI-EAS337_3:7:1:447:1231;identity=100\n-C08HBa0165B06_LR218\tS-MART\ttranscript\t8558\t8593\t36\t+\t.\tName=HWI-EAS337_3:7:1:538:1054;nbMismatches=1;feature=transcript;score=36;bestRegion=(self);nbGaps=0;nbOccurrences=1;quality=37;ID=HWI-EAS337_3:7:1:538:1054;identity=97\n' |
| b |
| diff -r 94ab73e8a190 -r 9bcfa7936eec SMART/data/test_clusterize2.gff3 --- a/SMART/data/test_clusterize2.gff3 Mon Apr 29 03:20:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,214 +0,0 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