| Next changeset 1:ebe5ec2e244d (2017-09-23) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c |
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added:
probecoverage.r probecoverage.xml test-data/coverage.tab test-data/graph.pdf test-data/probes.bed test-data/sample1 test-data/sample2 test-data/sample3 |
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| diff -r 000000000000 -r dbeb4a0abfc6 probecoverage.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/probecoverage.r Sat Sep 23 05:11:49 2017 -0400 |
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| @@ -0,0 +1,61 @@ +## Setup R error handling to go to stderr +options( show.error.messages=F, + error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +warnings() +library(optparse) +library(ggplot2) +library(reshape2) + +option_list <- list( + make_option(c("-i", "--input"), type="character", help="Path to dataframe"), + make_option(c("-t", "--title"), type="character", help="Main Title"), + make_option("--xlab", type = "character", help="X-axis legend"), + make_option("--ylab", type = "character", help="Y-axis legend"), + make_option("--sample", type = "character", help="a space separated of sample labels"), + make_option(c("-o", "--output"), type = "character", help="path to the pdf plot") + ) + +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) +args = parse_args(parser) +samples = substr(args$sample, 2, nchar(args$sample)-2) +samples = strsplit(samples, ", ") + +# data frames implementation + +Table <- read.delim(args$input, header=F) +headers = c("chromosome", "start", "end", "id") +for (i in seq(1, length(Table)-4)) { + headers <- c(headers, samples[[1]][i]) +colnames(Table) <- headers +} + +## function + +cumul <- function(x,y) sum(Table[,y]/(Table$end-Table$start) > x)/length(Table$chromosome) + +## end of function +## let's do a dataframe before plotting +maxdepth <- trunc(max(Table[,5:length(Table)]/(Table$end-Table$start))) + 20 +graphpoints <- data.frame(1:maxdepth) +i <- 5 +for (colonne in colnames(Table)[5:length(colnames(Table))]) { + graphpoints <- cbind(graphpoints, mapply(cumul, 1:maxdepth, rep(i, maxdepth))) + i <- i + 1 + } +colnames(graphpoints) <- c("Depth", colnames(Table)[5:length(Table)]) +maxfrac = max(graphpoints[,2:length(graphpoints)]) + +graphpoints <- melt(graphpoints, id.vars="Depth", variable.name="Samples", value.name="sample_value") + +## GRAPHS + +pdf(file=args$output) +ggplot(data=graphpoints, aes(x=Depth, y=sample_value, group=Samples, colour=Samples)) + + geom_line(size=1) + + scale_x_continuous(trans='log2', breaks = 2^(seq(0,log(maxdepth, 2)))) + + scale_y_continuous(breaks = seq(0, maxfrac, by=maxfrac/10)) + + labs(x=args$xlab, y=args$ylab, title=args$title) + + theme(legend.position="top", legend.title=element_blank(), legend.text=element_text(colour="blue", size=7)) + +devname=dev.off() + |
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| diff -r 000000000000 -r dbeb4a0abfc6 probecoverage.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/probecoverage.xml Sat Sep 23 05:11:49 2017 -0400 |
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| @@ -0,0 +1,84 @@ +<tool id="probecoverage" name="Probe Coverage" version="0.1.0"> + <description></description> + <requirements> + <requirement type="package" version="1.4.1">samtools</requirement> + <requirement type="package" version="2.26.0">bedtools</requirement> + <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement> + <requirement type="package" version="2.2.1=r3.3.1_0">r-ggplot2</requirement> + <requirement type="package" version="1.4.2=r3.3.1_0">r-reshape2</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + #for $file in $inputs + samtools index '$file' && + #end for + bedtools multicov + -bams + #for $file in $inputs + '$file' + #end for + -bed '$bed' > $bedtools_table && + Rscript '$__tool_directory__'/probecoverage.r + --input '$bedtools_table' + --title 'Probe coverage depth (cumulative distribution)' + --xlab 'Depth' + --ylab 'Fraction of covered regions with coverage >= Depth' + --output '$distribution' + --sample " + #for $file in $inputs + $file.element_identifier, + #end for + " + + ]]></command> + <inputs> + <param name="inputs" type="data" format="bam" label="Select multiple Bam alignments to parse" multiple="True"/> + <param name="bed" type="data" format="bed" label="Select a bed file describing the genomic regions to analyze" /> + </inputs> + + <outputs> + <data format="tabular" name="bedtools_table" label="bedtools multicov output" /> + <data format="pdf" name="distribution" label="Cumulative distribution of region coverages" /> +</outputs> + + <tests> + <test> + <param name="inputs" value="sample1,sample2,sample3" ftype="bam"/> + <param name="bed" value="probes.bed" ftype="bed"/> + <output file="coverage.tab" name="bedtools_table" /> + <output file="graph.pdf" name="distribution" /> + </test> + </tests> + + +<help> + +**What it does** + +Generates counts of alignments from multiple position-sorted BAM files +that overlap intervals in a BED file. + +Shows data as a cumulative plot of numbers of regions with coverage > x. + +**Inputs** + +bam alignment files that must be + + - sorted + - mapped to the same reference + +**Output** + +A data frame of computed counts + +A pdf file generated by R + +</help> + +<citations> + <citation type="doi">10.1093/bioinformatics/btq033</citation> +</citations> +</tool> + |
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| diff -r 000000000000 -r dbeb4a0abfc6 test-data/coverage.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage.tab Sat Sep 23 05:11:49 2017 -0400 |
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| b'@@ -0,0 +1,781 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| diff -r 000000000000 -r dbeb4a0abfc6 test-data/graph.pdf |
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| Binary file test-data/graph.pdf has changed |
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| diff -r 000000000000 -r dbeb4a0abfc6 test-data/probes.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/probes.bed Sat Sep 23 05:11:49 2017 -0400 |
| b |
| b'@@ -0,0 +1,781 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_chrX_49856786_f;uc004dot.1_exon_10_0_chrX_49856786_f;uc031tjo.1_exon_11_0_chrX_49856786_f\n+chrX\t49861667\t49862218\tuc004doq.1_exon_14_0_chrX_49856786_f;uc004dor.1_exon_14_0_chrX_49856786_f;uc004dos.1_exon_11_0_chrX_49856786_f;uc004dot.1_exon_10_0_chrX_49856786_f;uc031tjo.1_exon_11_0_chrX_49856786_f\n+chrX\t49862222\t49863932\tuc004doq.1_exon_14_0_chrX_49856786_f;uc004dor.1_exon_14_0_chrX_49856786_f;uc004dos.1_exon_11_0_chrX_49856786_f;uc004dot.1_exon_10_0_chrX_49856786_f;uc031tjo.1_exon_11_0_chrX_49856786_f\n+chrX\t128674224\t128674478\tuc004euq.3_exon_0_0_chrX_128674252_f;uc004eur.3_exon_0_0_chrX_128674252_f\n+chrX\t128674679\t128674822\tuc004euq.3_exon_1_0_chrX_128674721_f;uc004eur.3_exon_1_0_chrX_128674721_f\n+chrX\t128678889\t128679038\tuc004euq.3_exon_2_0_chrX_128678935_f;uc004eur.3_exon_2_0_chrX_128678935_f\n+chrX\t128682479\t128682621\tuc004euq.3_exon_3_0_chrX_128682540_f;uc004eur.3_exon_3_0_chrX_128682540_f\n+chrX\t128691279\t128691450\tuc004euq.3_exon_4_0_chrX_128691302_f;uc004eur.3_exon_4_0_chrX_128691302_f\n+chrX\t128691809\t128691945\tuc004euq.3_exon_5_0_chrX_128691838_f;uc004eur.3_exon_5_0_chrX_128691838_f\n+chrX\t128692584\t128692748\tuc004euq.3_exon_6_0_chrX_128692610_f;uc004eur.3_exon_6_0_chrX_128692610_f\n+chrX\t128692794\t128693002\tuc004euq.3_exon_7_0_chrX_128692817_f;uc004eur.3_exon_7_0_chrX_128692817_f\n+chrX\t128694504\t128694640\tuc004euq.3_exon_8_0_chrX_128694527_f;uc004eur.3_exon_8_0_chrX_128694527_f\n+chrX\t128695129\t128695300\tuc004euq.3_exon_9_0_chrX_128695156_f;uc004eur.3_exon_9_0_chrX_128695156_f\n+chrX\t128696329\t128696513\tuc004euq.3_exon_10_0_chrX_128696361_f;uc004eur.3_exon_10_0_chrX_128696361_f\n+chrX\t128696554\t128696799\tuc004euq.3_exon_11_0_chrX_128696576_f;uc004eur.3_exon_11_0_chrX_128696576_f\n+chrX\t128699724\t128699891\tuc004euq.3_exon_12_0_chrX_128699749_f;uc004eur.3_exon_12_0_chrX_128699749_f\n+chrX\t128701204\t128701373\tuc004euq.3_exon_13_0_chrX_128701231_f;uc004eur.3_exon_13_0_chrX_128701231_f\n+chrX\t128703209\t128703395\tuc004euq.3_exon_14_0_chrX_128703241_f;uc004eur.3_exon_14_0_chrX_128703241_f\n+chrX\t128709089\t128709193\tuc004euq.3_exon_15_0_chrX_128709117_f;uc004eur.3_exon_15_0_chrX_128709117_f\n+chrX\t128709839\t128710056\tuc004euq.3_exon_16_0_chrX_128709874_f;uc004eur.3_exon_16_0_chrX_128709874_f\n+chrX\t128710269\t128710542\tuc004euq.3_exon_17_0_chrX_128710294_f;uc004eur.3_exon_17_0_chrX_128710294_f\n+chrX\t128718259\t128718394\tuc004euq.3_exon_18_0_chrX_128718321_f\n+chrX\t128720954\t128721127\tuc004euq.3_exon_19_0_chrX_128720979_f;uc004eur.3_exon_18_0_chrX_128720979_f\n+chrX\t128722114\t128722271\tuc004euq.3_exon_20_0_chrX_128722156_f;uc004eur.3_exon_19_0_chrX_128722156_f\n+chrX\t128722829\t128723018\tuc004euq.3_exon_21_0_chrX_128722863_f;uc004eur.3_exon_20_0_chrX_128722863_f;uc010nrb.3_exon_0_0_chrX_128722863_f\n+chrX\t128723789\t128723974\tuc004euq.3_exon_22_0_chrX_128723822_f;uc004eur.3_exon_21_0_chrX_128723822_f\n+chrX\t128724099\t128725469\tuc004euq.3_exon_23_0_chrX_128724123_f;uc004eur.3_exon_22_0_chrX_128724123_f;uc010nrb.3_exon_1_0_chrX_128724123_f\n+chrX\t128725474\t128726564\tuc004euq.3_exon_23_0_chrX_128724123_f;uc004eur.3_exon_22_0_chrX_128724123_f;uc010nrb.3_exon_1_0_chrX_128724123_f\n' |
| b |
| diff -r 000000000000 -r dbeb4a0abfc6 test-data/sample1 |
| b |
| Binary file test-data/sample1 has changed |
| b |
| diff -r 000000000000 -r dbeb4a0abfc6 test-data/sample2 |
| b |
| Binary file test-data/sample2 has changed |
| b |
| diff -r 000000000000 -r dbeb4a0abfc6 test-data/sample3 |
| b |
| Binary file test-data/sample3 has changed |