| Next changeset 1:253c9448f524 (2019-06-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b |
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added:
crosscontamination_barcode_filter.xml scripts/batch_plotting_functions.R scripts/config_assertions.R scripts/contamination_plot.R scripts/crosscontamination_filter.R scripts/reorder_matrix_headers.R static/images/crosscontam_pretopost.png test-data/celseq_barcodes.192.raw test-data/out3.subtable test-data/test.pdf test-data/test.table |
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| diff -r 000000000000 -r 582b7bd4ae4c crosscontamination_barcode_filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crosscontamination_barcode_filter.xml Thu Jan 24 09:52:58 2019 -0500 |
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| b'@@ -0,0 +1,247 @@\n+<tool id="crosscontamination_barcode_filter" name="Cross-contamination Barcode Filter" version="@VERSION@">\n+ <description>for use in plate-based barcoded analyses</description>\n+ <macros>\n+ <token name="@VERSION@">0.1</token>\n+ <macro name="assert_conts" >\n+ <assert_contents>\n+ <has_text text="/CreationDate" />\n+ <has_text text="/Producer" />\n+ <has_line line="startxref" />\n+ <has_line line="%%EOF" />\n+ </assert_contents>\n+ </macro>\n+ <macro name="sanitize_batch">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.digits">\n+ <add value=","/>\n+ </valid>\n+ </sanitizer>\n+ </macro>\n+ <macro name="sanitize_regex">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.letters,string.digits">\n+ <add value="!"/>\n+ <add value="="/>\n+ <add value="-"/>\n+ <add value="."/>\n+ <add value="*"/>\n+ <add value="?"/>\n+ <add value="+"/>\n+ <add value="\\\\"/>\n+ <add value="_"/>\n+ <add value="["/> <!-- left square bracket, e.g subselecting from vec[1] -->\n+ <add value="]"/> <!-- right square bracket -->\n+ <add value="("/> <!-- left parenthesis -->\n+ <add value=")"/> <!-- right parenthesis -->\n+ </valid>\n+ </sanitizer>\n+ </macro> \n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="2.2.1" >r-ggplot2</requirement>\n+ </requirements>\n+ <version_command><![CDATA[\n+ Rscript \'$__tool_directory__/scripts/crosscontamination_filter.R\' | head -1 | cut -d\' \' -f 2\n+ ]]></version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ Rscript \'$__tool_directory__/scripts/crosscontamination_filter.R\' \'$crossconf\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="crossconf"><![CDATA[\n+script.dir = \'$__tool_directory__/scripts\'\n+input_matrix <- read.table(\n+ \'$input_table\',\n+ stringsAsFactors = F,\n+ na.strings=c("NA", "-", "?", "."),\n+ header=TRUE,\n+ row.names=1\n+)\n+input_matrix[is.na(input_matrix)] <- 0\n+#if str($inbuilt_spec.select_use) == "mpi_sagar":\n+spec = list(\n+ barcodes = \'$input_barcodes\',\n+ format = list(\n+ "1-96" = c(1,3,5,7),\n+ "97-192" = c(2,4,6,8)\n+ ),\n+ plates = list(\n+ "1" = c(1,2,3,4),\n+ "2" = c(5,6,7,8)\n+ )\n+)\n+#elif str($inbuilt_spec.select_use) == "custom":\n+spec = list(\n+ barcodes = \'$input_barcodes\',\n+ format = list(\n+ #for $i, $s in enumerate($inbuilt_spec.barcode_format)\n+ "${s.range_start}-${s.range_end}" = c( ${s.batches} ) \n+ #if $i < len(list($inbuilt_spec.barcode_format)) - 1\n+ ,\n+ #end if\n+ #end for\n+ ),\n+ plates = list(\n+ #for $i, $s in enumerate($inbuilt_spec.plate_format)\n+ "${s.plate}" = c( ${s.batches} )\n+ #if $i < len(list($inbuilt_spec.plate_format)) - 1\n+ ,\n+ #end if\n+ #end for\n+ )\n+)\n+#end if\n+regex.extract = \'$advanced.regex_extract\'\n+regex.display = \'$advanced.regex_display\'\n+out.pdf = \'$out_plots\'\n+out.table = \'$out_table\'\n+]]>\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="input_table" type="data" format="tsv,tabular" label="Input Matrix" />\n+ <param name="input_barcodes" type="data" format="tsv,tabular,txt" label="Complete Barcodes" />\n+ <conditional name="inbuilt_spec" >\n+ <param name="select_use" type="select" label="Plate Protocol" >\n+ <option value="mpi_sagar">CelSeq2 Plate Protocol (Sagar)</option>\n+ <option value="custom">Custom</option>\n+ </param>\n+ <whe'..b'ditional name="inbuilt_spec" >\n+ <param name="select_use" value="mpi_sagar" />\n+ </conditional>\n+ <output name="out_plots" >\n+ <expand macro="assert_conts" />\n+ </output>\n+ <output name="out_table" value="test.table" />\n+ </test>\n+ <test><!-- Plate and Lane test -->\n+ <param name="input_table" value="out3.subtable" />\n+ <param name="input_barcodes" value="celseq_barcodes.192.raw" />\n+ <conditional name="inbuilt_spec" >\n+ <param name="select_use" value="custom" />\n+ <repeat name="barcode_format" >\n+ <param name="range_start" value="1"/>\n+ <param name="range_end" value="96" />\n+ <param name="batches" value="1,3,5,7" />\n+ </repeat>\n+ <repeat name="barcode_format" >\n+ <param name="range_start" value="97"/>\n+ <param name="range_end" value="192" />\n+ <param name="batches" value="2,4,6,8" />\n+ </repeat>\n+ <repeat name="plate_format" >\n+ <param name="plate" value="1" />\n+ <param name="batches" value="1,2,3,4" />\n+ </repeat>\n+ <repeat name="plate_format" >\n+ <param name="plate" value="2" />\n+ <param name="batches" value="5,6,7,8" />\n+ </repeat>\n+ </conditional>\n+ <output name="out_plots" >\n+ <expand macro="assert_conts" />\n+ </output>\n+ <output name="out_table" value="test.table" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Cross-contamination Filter Plot\n+###################################\n+\n+For a set of barcodes and an experimental setup that uses a subset of these barcodes for each batch, this tool compares each batch against the full range of barcodes in order to determine whether any cross-contamination between batches has occured.\n+\n+If a significant number of transcripts are shown in a batch for cell barcodes that were not designed for that batch, then this tool will show that. In the below plot, we can see that there is no significant cross-contamination taking place (pre-filter), and so we can filter out the false barcodes (post-filter).\n+\n+.. image:: $PATH_TO_IMAGES/crosscontam_pretopost.png\n+ :scale: 50 %\n+\n+\n+Example\n+~~~~~~~~\n+\n+Consider the following experimental setup, with a list of 100 possible barcodes, used over 3 sequencing plates, with each plate containing 4 unique batches, and each plate using a specific subset of the 100 barcodes.\n+\n+:: \n+\n+ Barcodes\n+ \n+ 1 - 10 | AAA AAC AAT AAG ACA AGA ATA CAC GAG TAT\n+ 11 - 20 | CCC CCA CCT CCG CTC CGC TCT GCG TCT CGT\n+ .\n+ .\n+ 91 -100 | TTT TAT TCT TGT TTA TTC TTG TCC TGG TAA\n+\n+\n+\n+ Plate 1 +-------+-------+-------+-------+\n+ | B1 | B2 | B3 | B4 |\n+ +-------+-------+-------+-------+\n+ 1-50 51-100 51-100 1-50 \n+\n+ Plate 2 +-------+-------+-------+-------+\n+ | B5 | B6 | B7 | B8 |\n+ +-------+-------+-------+-------+\n+ 1-40 41-80 1-40 41-80\n+\n+ Plate 3 +-------+-------+-------+-------+\n+ | B9 | B10 | B11 | B12 |\n+ +-------+-------+-------+-------+\n+ 1-40 41-80 1-40 41-80 \n+\n+\n+****\n+\n+The above plate and barcoding setup can be more textually represented by specifying barcode ranges and plate numbers, with each denoting which batch numbers they describe as outlined below:\n+\n+::\n+\n+ *Barcodes \xe2\x86\x92 Batches*\n+ 1- 50: B1, B4\n+ 51-100: B2, B3\n+ 1- 40: B5, B7, B9 , B11\n+ 41- 80: B6, B8, B10, B12\n+\n+ *Plates \xe2\x86\x92 Batches*\n+ 1: B1, B2 , B3 , B4\n+ 2: B5, B6 , B7 , B8\n+ 3: B9, B10, B11, B12\n+\n+]]></help>\n+ <citations>\n+ <citation type="doi">10.1007/978-1-4939-7768-0_15</citation>\n+ </citations>\n+</tool>\n+\n' |
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| diff -r 000000000000 -r 582b7bd4ae4c scripts/batch_plotting_functions.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/batch_plotting_functions.R Thu Jan 24 09:52:58 2019 -0500 |
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| @@ -0,0 +1,95 @@ +#!/usr/bin/env R + +## +## Batch Plotting Functions +## +calculatePlateIndexes <- function(plate.form, full.barcode.size, num.plates){ + #' Determine plotting positions of plate lines (under false model) + #' + #' Assumes all plates are the same size and span the full range of the + #' barcodes. + #' + #' @param plate.form list of vectors mapping plates to batches + #' @param full.barcode.size size of the complete barcodes list + #' @param num.plates, number of plates + #' @return sequence of discrete plate-boundary positions + batches.per.plate <- length(plate.form[[1]]) + plate.size <- batches.per.plate * full.barcode.size + + return(seq(0, num.plates * plate.size, plate.size)) +} + + +calculateFullBarcodeIndexes <- function(num.batches, full.barcode.size){ + #' Determines plotting position of batch lines (under false model) + #' + #' For N batches and a list of actually detected barcodes in the header, + #' generates where the blue lines should be + #' + #' @param num.batches number of batches in experiment + #' @param full.barcode.size size of all barcodes + #' @return sequence of discrete batch positions + bsize <- full.barcode.size + return(seq(0, num.batches * bsize, bsize)) +} + + + +calculateRealBarcodeIndexes <- function(barcode.form, full.barcode.size){ + #' Determine plotting position of the true batch lines (under true model) + #' + #' For N batches a list of actually USED barcodes as given by the spec, + #' generates where the green lines should be + #' + #' @param barcode.form list of barcode formats and the batches they map to + #' @param full.barcode.size size of all barcodes + #' @return list of useful vectors: true batch positions using whole matrix, + #' true batch positions using the filtered matrix which contains + #' only real barcodes, and a list of batches and their respective + #' sizes. + batches <- c() + res <- sapply(names(barcode.form), function(key){ + rng <- as.integer(unlist(strsplit(key, '-'))) + size.of.range <- length(seq(rng[1],rng[2])) + sub.batches <- barcode.form[[key]] # 1,3,5,7 or 2,4,6,8 + res2 <- lapply(sub.batches, function(bat){ + batches[[bat]] <<- size.of.range + }) + }) + ## We now have sizes per batch, in order of batch + ## Need to place these at positions after each full barcode size + positions <- c() + real_positions <- c(0) + + res <- sapply(1:length(batches), function(b){ + batch.start <- (b-1) * full.barcode.size + batch.size <- batches[[b]] + positions <<- c(positions, batch.start + batch.size) + real_positions[[b+1]] <<- batch.size + real_positions[[b]] + }) + + real_positions <- real_positions[2:length(real_positions)] + + return(list(unfiltered=positions,filtered=real_positions, batches=batches)) +} + +calculateRealPlateIndexes <- function(plate.form, batches, num.plates){ + #' Determine true plate positions given variable batch sizes + #' + #' Given the true size of each batch, and which batches exist in which plates + #' calculate the size of each plate + #' + #' @param plate.form list of vectors mapping plates to batches + #' @param batches list of batches and their respective sizes + #' @param num.plates number of plates + #' @return sequence of plate positions + batches.per.plate <- length(plate.form[[1]]) + + size.of.plate <- 0 + res <- sapply(plate.form[[1]], function(batch){ + batch.size <- batches[[batch]] + size.of.plate <<- size.of.plate + batch.size + }) + + return(seq(0, num.plates * size.of.plate, size.of.plate)) +} |
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| diff -r 000000000000 -r 582b7bd4ae4c scripts/config_assertions.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/config_assertions.R Thu Jan 24 09:52:58 2019 -0500 |
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| @@ -0,0 +1,91 @@ +#!/usr/bin/env R +## +## Sanity Check Methods +## +checkNoMissingRanges <- function(format, barcodes){ + #' Checks coverage of barcodes across all specified ranges + #' + #' e.g. 1-50, 60-80 -- barcodes 51-59 are not specified. This + #' is not a fatal error, but a warning is issued. + #' + #' @param format barcode range and the batches they map to + #' @param barcodes full list of barcodes + #' @return list of specified barcodes + ranges <- c() + res <- sapply(names(format), function(key){ + rng <- as.integer(unlist(strsplit(key, '-'))) + ranges <<- c(ranges, seq(rng[1],rng[2])) + }) + full.range <- seq(min(ranges),max(ranges)) + not.in <- !(full.range %in% ranges) + if (sum(not.in) != 0) { + message("Warning: values[", + paste(full.range[not.in], collapse=","), + "] -> barcodes[", + paste(barcodes[not.in], collapse=","), + "] are not used." + ) + } else { + message("All barcodes accounted for.") + } + return(barcodes[!not.in]) +} + +checkNoMissingBarcodes <- function(headers, barcodes){ + #' Extracts barcodes in the headers and compares them with those in barcodes + #' + #' @param headers matrix headers, must be of P1_B2_ACTG format + #' @param barcodes full list of barcodes + barcs.in.matrix <- unique(sort(sub(".*_.*_([ACTG]+)", "\\1", headers))) + not.in <- !(barcs.in.matrix %in% barcodes) + if (sum(not.in) > 0){ + message("Warning: Barcodes in matrix not in barcodes file\n", barcs.in.matrix[not.in]) + } else { + message("All input matrix barcodes accounted for.") + } +} + +assertNoMissingBatches <- function(format, plates){ + #' Checks the barcode and plate spec match + #' + #' These must specify the same batches. + #' + #' @param format barcode format, ranges to batches + #' @param plates plate format, plates to batches + #' @return number of batches + batches.form = c() + batches.plate = c() + for (form in format){batches.form = c(batches.form, form)} + for (plate in plates){batches.plate = c(batches.plate, plate)} + + if (length(batches.plate) != length(batches.form)){ + stop("Error: The number of batches specified in the plate do not match those given in the barcode format") + } + + range.form <- seq(min(batches.form), max(batches.form)) + range.plate <- seq(min(batches.plate), max(batches.plate)) + + if (sum(!(range.form %in% batches.form)) > 0){ + stop("Error: Missing batch in barcode format") + } + if (sum(!(range.plate %in% batches.plate)) > 0){ + stop("Error: Missing batch in plate format") + } + return(length(range.form)) +} + +sanityCheck <- function(spec, matrix.headers){ + #' Checks specification and matrix headers for consistency + #' + #' @param spec experiment specification + #' @param matrix.headers column names of input matrix + #' @return list of barcodes, as well as number of barcodes, plates, and batches + barcodes <- scan(spec$barcodes, what="", sep="\n") + num.barcodes <- length(barcodes) + num.plates <- length(names(spec$plate)) + used.barcodes <- checkNoMissingRanges(spec$format, barcodes) + num.batches <- assertNoMissingBatches(spec$format, spec$plates) + checkNoMissingBarcodes(matrix.headers, used.barcodes) + + return(list(barc=barcodes, barc.n=num.barcodes, plates.n=num.plates, batch.n=num.batches)) +} |
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| diff -r 000000000000 -r 582b7bd4ae4c scripts/contamination_plot.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/contamination_plot.R Thu Jan 24 09:52:58 2019 -0500 |
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| @@ -0,0 +1,140 @@ +#!/usr/bin/env R + +require(ggplot2) + +log10histoPlot <- function(columncounts, title=""){ + #' Log10 histogram plot + #' + #' @param columncounts colSums(input_matrix) + #' @param title Title of plot + #' @return ggplot grob + dfer <- data.frame(colcounts=log10(columncounts)) + p1 <- ggplot(dfer, aes(x=colcounts)) + + geom_histogram(binwidth = 0.05, color="black",fill="white") + + theme(plot.title = element_text(hjust = 0.5)) + + labs(title=title, y="Frequency", x="Library Size (Log10)") + + return(p1) +} + +contaminationPlot <- function(columncounts, title = "", + indexes.plates, indexes.fullbc, indexes.truebc, + filtered=FALSE) +{ + #' Plots true and false barcodes + #' + #' + #' @param columncounts colSums(input_matrix) + #' @param title plot title + #' @param indexes.plates plate line positions + #' @param indexes.fullbc full batch line positions + #' @param indexes.truebc true batch line positions + #' @param filtered specifies whether the positions have been adjusted for true barcodes + #' @return ggplot grob + dfer <- data.frame(colcounts=columncounts) + + ## Remove indexes where plates and full barcodes mix + indexes.fullbc = indexes.fullbc[!(indexes.fullbc %in% indexes.plates)] + + nit <- length(indexes.truebc) + nif <- length(indexes.fullbc) + nip <- length(indexes.plates) + mval <- max(dfer) + + ## Aesthetics + min.height <- -200 + tf.spacing.left <- 12 + tf.spacing.right <- 12 + tf.height <- mval - 10000 + bn.height <- mval - 2000 + plate.color <- "grey" + plate.text.color <- "black" + plate.text.alpha <- 0.5 + plate.text.size <- 3 + plate.height <- 2* mval / 5 + plate.spacing <- if (filtered) 12 else 24 + plate.height.text <- plate.height - 3000 + + truebcs <- data.frame( + x=indexes.truebc, y=rep(min.height,nit), + xend=indexes.truebc, yend=rep(mval,nit) + ) + fullbcs <- data.frame( + x=indexes.fullbc, y=rep(min.height,nif), + xend=indexes.fullbc, yend=rep(mval,nif) + ) + platess <- data.frame( + x=indexes.plates, y=rep(min.height,nip), + xend=indexes.plates, yend=rep(plate.height,nip) + ) + connecting.bar <- data.frame( + xsta = min(indexes.plates), ysta = min.height, + xfin = max(indexes.plates), yfin = min.height + ) + + p1 <- ggplot() + + if (!filtered){ + p1 <- p1 + + geom_segment(data=truebcs, aes(x=x,y=y,xend=xend,yend=yend - 4000), col='grey', lty=2, size=0.2) + + geom_segment(data=fullbcs, aes(x=x,y=y,xend=xend,yend=yend), col='blue', lty=1, size=0.4, alpha=0.2) + } + else { + p1 <- p1 + + geom_segment(data=truebcs, aes(x=x,y=y,xend=xend,yend=yend), col='blue', lty=1, size=0.4, alpha=0.2) + } + + p1 <- p1 + + geom_segment(data=platess, aes(x=x,y=y,xend=xend,yend=yend), col=plate.color, lty=1, size=1) + + geom_segment(data=connecting.bar, aes(x=xsta,y=ysta,xend=xfin,yend=yfin), col=plate.color, lty=1, size=1) + + geom_point( + data=dfer, aes(x=1:length(rownames(dfer)), y=dfer$colcounts), + pch = 16, cex = 1) + + theme(plot.title = element_text(hjust = 0.5), + axis.ticks.x=element_blank(), axis.ticks.y=element_blank(), + axis.text.x=element_blank()) + + labs(title=paste("Contamination Plot\n", title), y="Library Size", x="Barcode Index") + + scale_y_continuous(breaks=seq(0,mval + 10000, 10000)) + + scale_x_continuous(breaks=NULL) + + ## Add true/false and batch labels + res <- lapply(indexes.truebc, function(xval){ + batch <- match(xval, indexes.truebc) + + if (!filtered){ + p1 <<- p1 + + annotate("text", x=xval - tf.spacing.left, size=2, y=tf.height, angle=90, label=" true positives", color = "dark blue", alpha = 0.5) + + annotate("text", x=xval + tf.spacing.right, size=2, y=tf.height, angle=-90,label="false positives", color = "black", alpha = 0.5) + + annotate("text", x=xval , size=4, y=bn.height, angle=-90, label=paste("B",batch,sep=""), color = "grey", alpha = 0.8) + } + else { + p1 <<- p1 + + annotate("text", x=xval - 48, size=4, y=bn.height, angle=-90, label=paste("B",batch,sep=""), color = "grey", alpha = 0.8) + } + }) + + ## Add Plate labels + res <- lapply(indexes.plates, function(p){ + plate.num <- match(p, indexes.plates) + c.label <- paste("Plate", plate.num, sep="") + b.label <- paste("Plate", plate.num - 1, sep="") + + # Right label + if (plate.num < length(indexes.plates)){ + p1 <<- p1 + + annotate("text", x=p + plate.spacing, size=plate.text.size, y=plate.height.text, angle=-90, + label=c.label, color = plate.text.color, alpha=plate.text.alpha) + } + + # Left label + if (plate.num > 1){ + p1 <<- p1 + + annotate("text", x=p - plate.spacing, size=plate.text.size, y=plate.height.text, angle=90, + label=b.label, color = plate.text.color, alpha=plate.text.alpha) + } + }) + + return(p1) +} + + |
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| diff -r 000000000000 -r 582b7bd4ae4c scripts/crosscontamination_filter.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/crosscontamination_filter.R Thu Jan 24 09:52:58 2019 -0500 |
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| @@ -0,0 +1,73 @@ +#!/usr/bin/env R +VERSION = "0.1" + +args = commandArgs(trailingOnly = T) + +if (length(args) != 1){ + message(paste("VERSION:", VERSION)) + stop("Please provide the config file") +} + +source(args[1]) +source(file.path(script.dir, "config_assertions.R")) +source(file.path(script.dir, "batch_plotting_functions.R")) +source(file.path(script.dir, "reorder_matrix_headers.R")) +source(file.path(script.dir, "contamination_plot.R")) + + +colnames(input_matrix) <- convertHeadersToSensible( + regex.extract, + regex.display, + colnames(input_matrix) +) + +sc <- sanityCheck(spec, colnames(input_matrix)) + +barcodes <- sc$barc +num.barcodes <- sc$barc.n +num.batches <- sc$batch.n +num.plates <- sc$plates.n + +real.indexes = calculateRealBarcodeIndexes(spec$format, num.barcodes) +plate.indexes = calculatePlateIndexes(spec$plates, num.barcodes, num.plates) +plate.indexes.real = calculateRealPlateIndexes(spec$plates, real.indexes$batches, num.plates) + +ordering <- reorderMatrixHeaders(barcodes, colnames(input_matrix), spec$format) + +## Unfiltered +nmatrix <- input_matrix[,ordering$all] + +plot.prefilter <- contaminationPlot( + colSums(nmatrix), + title="Pre-Filter", + plate.indexes, + calculateFullBarcodeIndexes(num.batches, num.barcodes), + real.indexes$unfiltered +) + + +## Filtered +cmatrix <- input_matrix[,ordering$correct] + +plot.postfilter <- contaminationPlot( + colSums(cmatrix), + title="Post-Filter", + plate.indexes.real, + calculateFullBarcodeIndexes(num.batches, num.barcodes), + real.indexes$filtered, + filtered = T +) + +plot.histogram <- log10histoPlot( + colSums(cmatrix), + "Histogram of Post-Filter Matrix Counts" +) + +pdf(out.pdf) +plot.prefilter +plot.postfilter +plot.histogram +dev.off() + + +write.table(cmatrix, file=out.table, quote=FALSE, na="0", sep="\t") |
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| diff -r 000000000000 -r 582b7bd4ae4c scripts/reorder_matrix_headers.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/reorder_matrix_headers.R Thu Jan 24 09:52:58 2019 -0500 |
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| @@ -0,0 +1,61 @@ +#!/usr/bin/env R +## +## Reorder matrix +## +convertHeadersToSensible <- function(regex.from, regex.to, col.names){ + #' Strips headers of filenames and sets plate, batch, and barcodes + #' + #' @param regex.from format to extract plate, batch, and barcodes + #' @param regex.to format to set + #' @param matrix input matrix to rename headers + #' @return updated names + return(sub(regex.from, regex.to, col.names)) +} + +reorderMatrixHeaders <- function(barcodes, headers, barcode.format){ + #' Reorder headers to segment wanted and unwanted barcodes on opposite sides + #' of each batch + #' + #' @param barcodes list of full barcodes + #' @param headers input matrix headers + #' @param barcode.format batch list specifying valid barcodes for each batch + #' @return list of all barcodes sorted bilaterally by batch, and true barcodes + form <- barcode.format + batch.ordering <- list() + batch.ordering.correct <- list() + + res <- sapply(names(form), function(key){ + rng <- as.integer(unlist(strsplit(key, '-'))) + ranges <- seq(rng[1],rng[2]) + + barc.wanted <- barcodes[ranges] + barc.unwant <- barcodes[!(barcodes %in% barc.wanted)] + + sub.batches <- form[[key]] # 1,3,5,7 or 2,4,6,8 + res2 <- lapply(sub.batches, function(bat){ + batch_bar <- headers[grepl(paste("P\\d_B",bat,"_([ACGT]+)", sep=""), headers)] + barcs.in.batch <- sub("P._B._([ACGT]+)", "\\1", batch_bar) + b.wanted <- batch_bar[barcs.in.batch %in% barc.wanted] + b.unwant <- batch_bar[barcs.in.batch %in% barc.unwant] + + if (sum(b.wanted %in% b.unwant) > 0){ + stop("Barcode given twice!", b.wanted[b.wanted %in% b.unwant]) + } + barc_order <- c(b.wanted, b.unwant) + batch.ordering[[bat]] <<- barc_order + batch.ordering.correct[[bat]] <<- b.wanted + }) + }) + + barcode.ordering <- c() + barcode.ordering.correct <- c() + + res <- lapply(1:length(batch.ordering), function(bat){ + barc_order <- batch.ordering[[bat]] + barc_order.correct <- batch.ordering.correct[[bat]] + barcode.ordering <<- c(barcode.ordering, barc_order) + barcode.ordering.correct <<- c(barcode.ordering.correct, barc_order.correct) + }) + + return(list(all=barcode.ordering,correct=barcode.ordering.correct)) +} |
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| diff -r 000000000000 -r 582b7bd4ae4c static/images/crosscontam_pretopost.png |
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| Binary file static/images/crosscontam_pretopost.png has changed |
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| diff -r 000000000000 -r 582b7bd4ae4c test-data/celseq_barcodes.192.raw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/celseq_barcodes.192.raw Thu Jan 24 09:52:58 2019 -0500 |
| b |
| @@ -0,0 +1,192 @@ +AGTGTC +ACCATG +GAGTGA +CACTCA +CATGTC +ACAGGA +GTACCA +ACAGAC +ACGTTG +ACCAAC +GTGAAG +CACTTC +GAGTTG +GAAGAC +TGCAGA +CTAGGA +ACCAGA +GTGACA +CTAGAC +AGCTCA +ACTCGA +CTGTTG +CATGCA +CAGAAG +GTCTCA +GTGATC +TGTCTG +GACAGA +ACTCTG +TGCAAC +GAAGGA +GTTGAG +AGACCA +TGGTTG +GATCTG +CTAGTG +CTCAGA +CTTCGA +AGCTAG +GATCGA +GTACTC +TGTCGA +ACGTGA +AGGATC +CTCATG +AGACTC +GACAAC +AGGACA +ACTCAC +GTACAG +AGGAAG +AGTGCA +TGGTGA +AGACAG +AGCTTC +TGAGGA +ACGTAC +TCACAG +ACAGTG +CGATTG +TCTTGC +GGTAAC +TCATCC +TAGGAC +TTCACC +AACGAG +GTGGAA +ATGTCG +ATCACG +GAATCC +CGATGA +GAATGG +GCAACA +TTCTCG +ATTGCG +TAGTGG +AAGCCA +CTATCC +TCCGAA +TGAACC +TGTACG +GACGAA +CCACAA +CACCAA +CTAAGC +GATACG +ACAAGC +TGAAGG +TAACGG +AACCTC +CGTCTA +CCATAG +TTCCAG +GGACAA +ACTTCG +TTGTGC +GGTATG +CTGCTA +ATGAGG +GGTAGA +ATCGTG +ATGGAC +AGTAGG +CCATCA +AGTACC +CCAGTA +CGTTAC +GAGGTA +TTGGCA +CAATGC +GCGTTA +TAGCTC +TTCGAC +GAGCAA +TTGCTG +TTGCGA +GCAGAA +CCTACA +GCATGA +AACTGG +CGGTTA +CTAACG +CACGTA +TTGGAG +GCAATG +TATCCG +ATGCAG +GCTCTA +ATTCGC +TGTTGG +ATGACC +CCGTAA +TGATCG +TACAGG +AGAACG +GCCATA +ACGGTA +AAGCAC +CGAACA +ATGCTC +GGCTTA +ATCGCA +GGATCA +CCAATC +AAGGTG +ATCTCC +GTATCG +TGTTCC +GGTGTA +TACTCC +ATCAGC +AAGTGC +AGGCTA +CCTATG +TATCGC +CGCTAA +GTAACC +ACATGG +CCGATA +GGATAC +GTTAGG +TACGCA +AGATGC +TTGCAC +CAGGAA +TCTAGG +GCTTCA +TTGGTC +TACCGA +CATTGG +CTCGAA +GCTTAC +ATACGG +GTATGC +TGTAGC +CGTAAG +TTACGC +TACCAC +CGCATA +GCTAAG +ATCCAC +CCTTGA +AGCGAA +GGTTAG +GATTGC +CGTTCA +ATCCGA +GCATTC +CCTGAA +GGAATC +TCAACG +AACACC |
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| diff -r 000000000000 -r 582b7bd4ae4c test-data/out3.subtable --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out3.subtable Thu Jan 24 09:52:58 2019 -0500 |
| b |
| b'@@ -0,0 +1,176 @@\n+WD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AACACC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AACCTC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AACGAG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AACTGG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AAGCAC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AAGCCA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AAGGTG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AAGTGC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACAAGC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACAGAC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACAGGA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACAGTG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACATGG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACCAAC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACCAGA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACCATG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACGGTA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACGTAC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACGTGA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACGTTG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACTCAC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACTCGA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACTCTG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ACTTCG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGAACG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGACAG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGACCA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGACTC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGATGC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGCGAA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGCTAG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGCTCA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGCTTC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGGAAG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGGACA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGGATC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGGCTA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGTACC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGTAGG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGTGCA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_AGTGTC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATACGG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATCACG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATCAGC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATCCAC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATCCGA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATCGCA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATCGTG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATCTCC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATGACC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATGAGG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATGCAG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATGCTC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATGGAC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATGTCG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATTCGC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_ATTGCG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CAATGC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CACCAA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CACGTA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CACTCA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CACTTC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CAGAAG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CAGGAA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CATGCA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CATGTC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CATTGG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCAATC\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCACAA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCAGTA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCATAG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCATCA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCGATA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCGTAA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCTACA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCTATG\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCTGAA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CCTTGA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CGAACA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CGATGA\tWD_DP_120218_P1_1.fastq_WD_DP_120218_P1_1_CGATTG\tWD_DP_12021'..b'\t0\t0\t0\t7\t0\t0\t0\t0\t0\t1\t1\t0\t5\t1\t0\t0\t0\t3\t0\t1\t0\t2\t7\t1\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t2\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t2\t1\t0\t0\t5\t0\t0\t0\t0\t0\t1\t8\t6\t0\t0\t0\t0\t3\t2\t0\t0\t0\t8\t0\t0\t0\t1\t0\t0\t0\t1\t0\t1\t2\t0\t0\t0\t10\t0\t0\t0\t0\t0\t3\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t1\t9\t0\t0\t0\t0\t1\t0\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t1\t0\t2\t0\t1\t8\t1\t5\t0\t0\t0\t4\t2\t0\t4\t4\t5\t0\t2\t0\t0\t0\t0\t0\t1\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t2\t0\t0\t1\t0\t1\t0\t0\t1\t0\t0\t0\t1\t6\t0\t0\t0\t2\t4\t4\t0\t0\t0\t1\t0\t0\t0\t0\t2\t0\t5\t0\t0\t1\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t3\t1\t0\t2\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t3\t1\t0\t0\t2\t1\t4\t0\t2\t2\t0\t0\t1\t0\t0\t1\t0\t0\t0\t5\t0\t0\t0\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| diff -r 000000000000 -r 582b7bd4ae4c test-data/test.table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.table Thu Jan 24 09:52:58 2019 -0500 |
| b |
| b'@@ -0,0 +1,176 @@\n+P1_B1_AACCTC\tP1_B1_AACGAG\tP1_B1_AAGCCA\tP1_B1_ACAAGC\tP1_B1_ACAGAC\tP1_B1_ACAGGA\tP1_B1_ACAGTG\tP1_B1_ACCAAC\tP1_B1_ACCAGA\tP1_B1_ACCATG\tP1_B1_ACGTAC\tP1_B1_ACGTGA\tP1_B1_ACGTTG\tP1_B1_ACTCAC\tP1_B1_ACTCGA\tP1_B1_ACTCTG\tP1_B1_ACTTCG\tP1_B1_AGACAG\tP1_B1_AGACCA\tP1_B1_AGACTC\tP1_B1_AGCTAG\tP1_B1_AGCTCA\tP1_B1_AGCTTC\tP1_B1_AGGAAG\tP1_B1_AGGACA\tP1_B1_AGGATC\tP1_B1_AGTGCA\tP1_B1_AGTGTC\tP1_B1_ATCACG\tP1_B1_ATGTCG\tP1_B1_ATTGCG\tP1_B1_CACCAA\tP1_B1_CACTCA\tP1_B1_CACTTC\tP1_B1_CAGAAG\tP1_B1_CATGCA\tP1_B1_CATGTC\tP1_B1_CCACAA\tP1_B1_CCATAG\tP1_B1_CGATGA\tP1_B1_CGATTG\tP1_B1_CGTCTA\tP1_B1_CTAAGC\tP1_B1_CTAGAC\tP1_B1_CTAGGA\tP1_B1_CTAGTG\tP1_B1_CTATCC\tP1_B1_CTCAGA\tP1_B1_CTCATG\tP1_B1_CTGTTG\tP1_B1_CTTCGA\tP1_B1_GAAGAC\tP1_B1_GAAGGA\tP1_B1_GAATCC\tP1_B1_GAATGG\tP1_B1_GACAAC\tP1_B1_GACAGA\tP1_B1_GACGAA\tP1_B1_GAGTGA\tP1_B1_GAGTTG\tP1_B1_GATACG\tP1_B1_GATCGA\tP1_B1_GATCTG\tP1_B1_GCAACA\tP1_B1_GGACAA\tP1_B1_GGTAAC\tP1_B1_GTACAG\tP1_B1_GTACCA\tP1_B1_GTACTC\tP1_B1_GTCTCA\tP1_B1_GTGAAG\tP1_B1_GTGACA\tP1_B1_GTGATC\tP1_B1_GTGGAA\tP1_B1_GTTGAG\tP1_B1_TAACGG\tP1_B1_TAGGAC\tP1_B1_TAGTGG\tP1_B1_TCACAG\tP1_B1_TCATCC\tP1_B1_TCCGAA\tP1_B1_TCTTGC\tP1_B1_TGAACC\tP1_B1_TGAAGG\tP1_B1_TGAGGA\tP1_B1_TGCAAC\tP1_B1_TGCAGA\tP1_B1_TGGTGA\tP1_B1_TGGTTG\tP1_B1_TGTACG\tP1_B1_TGTCGA\tP1_B1_TGTCTG\tP1_B1_TTCACC\tP1_B1_TTCCAG\tP1_B1_TTCTCG\tP1_B1_TTGTGC\tP1_B2_AACACC\tP1_B2_AACTGG\tP1_B2_AAGCAC\tP1_B2_AAGGTG\tP1_B2_AAGTGC\tP1_B2_ACATGG\tP1_B2_ACGGTA\tP1_B2_AGAACG\tP1_B2_AGATGC\tP1_B2_AGCGAA\tP1_B2_AGGCTA\tP1_B2_AGTACC\tP1_B2_AGTAGG\tP1_B2_ATACGG\tP1_B2_ATCAGC\tP1_B2_ATCCAC\tP1_B2_ATCCGA\tP1_B2_ATCGCA\tP1_B2_ATCGTG\tP1_B2_ATCTCC\tP1_B2_ATGACC\tP1_B2_ATGAGG\tP1_B2_ATGCAG\tP1_B2_ATGCTC\tP1_B2_ATGGAC\tP1_B2_ATTCGC\tP1_B2_CAATGC\tP1_B2_CACGTA\tP1_B2_CAGGAA\tP1_B2_CATTGG\tP1_B2_CCAATC\tP1_B2_CCAGTA\tP1_B2_CCATCA\tP1_B2_CCGATA\tP1_B2_CCGTAA\tP1_B2_CCTACA\tP1_B2_CCTATG\tP1_B2_CCTGAA\tP1_B2_CCTTGA\tP1_B2_CGAACA\tP1_B2_CGCATA\tP1_B2_CGCTAA\tP1_B2_CGGTTA\tP1_B2_CGTAAG\tP1_B2_CGTTAC\tP1_B2_CGTTCA\tP1_B2_CTAACG\tP1_B2_CTCGAA\tP1_B2_CTGCTA\tP1_B2_GAGCAA\tP1_B2_GAGGTA\tP1_B2_GATTGC\tP1_B2_GCAATG\tP1_B2_GCAGAA\tP1_B2_GCATGA\tP1_B2_GCATTC\tP1_B2_GCCATA\tP1_B2_GCGTTA\tP1_B2_GCTAAG\tP1_B2_GCTCTA\tP1_B2_GCTTAC\tP1_B2_GCTTCA\tP1_B2_GGAATC\tP1_B2_GGATAC\tP1_B2_GGATCA\tP1_B2_GGCTTA\tP1_B2_GGTAGA\tP1_B2_GGTATG\tP1_B2_GGTGTA\tP1_B2_GGTTAG\tP1_B2_GTAACC\tP1_B2_GTATCG\tP1_B2_GTATGC\tP1_B2_GTTAGG\tP1_B2_TACAGG\tP1_B2_TACCAC\tP1_B2_TACCGA\tP1_B2_TACGCA\tP1_B2_TACTCC\tP1_B2_TAGCTC\tP1_B2_TATCCG\tP1_B2_TATCGC\tP1_B2_TCAACG\tP1_B2_TCTAGG\tP1_B2_TGATCG\tP1_B2_TGTAGC\tP1_B2_TGTTCC\tP1_B2_TGTTGG\tP1_B2_TTACGC\tP1_B2_TTCGAC\tP1_B2_TTGCAC\tP1_B2_TTGCGA\tP1_B2_TTGCTG\tP1_B2_TTGGAG\tP1_B2_TTGGCA\tP1_B2_TTGGTC\tP1_B3_AACCTC\tP1_B3_AACGAG\tP1_B3_AAGCCA\tP1_B3_ACAAGC\tP1_B3_ACAGAC\tP1_B3_ACAGGA\tP1_B3_ACAGTG\tP1_B3_ACCAAC\tP1_B3_ACCAGA\tP1_B3_ACCATG\tP1_B3_ACGTAC\tP1_B3_ACGTGA\tP1_B3_ACGTTG\tP1_B3_ACTCAC\tP1_B3_ACTCGA\tP1_B3_ACTCTG\tP1_B3_ACTTCG\tP1_B3_AGACAG\tP1_B3_AGACCA\tP1_B3_AGACTC\tP1_B3_AGCTAG\tP1_B3_AGCTCA\tP1_B3_AGCTTC\tP1_B3_AGGAAG\tP1_B3_AGGACA\tP1_B3_AGGATC\tP1_B3_AGTGCA\tP1_B3_AGTGTC\tP1_B3_ATCACG\tP1_B3_ATGTCG\tP1_B3_ATTGCG\tP1_B3_CACCAA\tP1_B3_CACTCA\tP1_B3_CACTTC\tP1_B3_CAGAAG\tP1_B3_CATGCA\tP1_B3_CATGTC\tP1_B3_CCACAA\tP1_B3_CCATAG\tP1_B3_CGATGA\tP1_B3_CGATTG\tP1_B3_CGTCTA\tP1_B3_CTAAGC\tP1_B3_CTAGAC\tP1_B3_CTAGGA\tP1_B3_CTAGTG\tP1_B3_CTATCC\tP1_B3_CTCAGA\tP1_B3_CTCATG\tP1_B3_CTGTTG\tP1_B3_CTTCGA\tP1_B3_GAAGAC\tP1_B3_GAAGGA\tP1_B3_GAATCC\tP1_B3_GAATGG\tP1_B3_GACAAC\tP1_B3_GACAGA\tP1_B3_GACGAA\tP1_B3_GAGTGA\tP1_B3_GAGTTG\tP1_B3_GATACG\tP1_B3_GATCGA\tP1_B3_GATCTG\tP1_B3_GCAACA\tP1_B3_GGACAA\tP1_B3_GGTAAC\tP1_B3_GTACAG\tP1_B3_GTACCA\tP1_B3_GTACTC\tP1_B3_GTCTCA\tP1_B3_GTGAAG\tP1_B3_GTGACA\tP1_B3_GTGATC\tP1_B3_GTGGAA\tP1_B3_GTTGAG\tP1_B3_TAACGG\tP1_B3_TAGGAC\tP1_B3_TAGTGG\tP1_B3_TCACAG\tP1_B3_TCATCC\tP1_B3_TCCGAA\tP1_B3_TCTTGC\tP1_B3_TGAACC\tP1_B3_TGAAGG\tP1_B3_TGAGGA\tP1_B3_TGCAAC\tP1_B3_TGCAGA\tP1_B3_TGGTGA\tP1_B3_TGGTTG\tP1_B3_TGTACG\tP1_B3_TGTCGA\tP1_B3_TGTCTG\tP1_B3_TTCACC\tP1_B3_TTCCAG\tP1_B3_TTCTCG\tP1_B3_TTGTGC\tP1_B4_AACACC\tP1_B4_AACTGG\tP1_B4_AAGCAC\tP1_B4_AAGGTG\tP1_B4_AAGTGC\tP1_B4_ACATGG\tP1_B4_ACGGTA\tP1_B4_AGAACG\tP1_B4_AGATGC\tP1_B4_AGCGAA\tP1_B4_AGGCTA\tP1_B4_AGTACC\tP1_B4_AGTAGG\tP1_B4_ATACGG\tP1_B4_ATCAGC\tP1_B4_ATCCAC\tP1_B4_ATCCGA\tP1_B4_ATCGCA\tP1'..b'\t0\t0\t0\t0\t0\t1\t7\t0\t0\t0\t3\t0\t1\t0\t55\t0\t9\t0\t0\t0\t0\t3\t5\t5\t4\t0\t3\t0\t1\t0\t0\t0\t0\t0\t0\t14\t0\t0\t47\t0\t0\t8\t1\t0\t26\t0\t6\t24\t0\t6\t6\t0\t0\t4\t19\t0\t1\t4\t0\t0\t9\t0\t11\t1\t19\t15\t0\t10\t39\t0\t0\t4\t0\t14\t1\t1\t0\t3\t3\t0\t0\t8\t1\t0\t9\t12\t0\t1\t15\t0\t30\t1\t2\t1\t5\t21\t2\t7\t0\t6\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t10\t0\t1\t0\t23\t0\t9\t2\t1\t4\t10\t0\t8\t1\t3\t0\t0\t0\t2\t0\t0\t0\t0\t2\t1\t1\t0\t6\t4\t0\t0\t0\t12\t1\t0\t2\t7\t34\t2\t0\t11\t4\t1\t0\t0\t1\t1\t4\t3\t0\t2\t7\t0\t0\t0\t0\t0\t12\t0\t0\t0\t0\t22\t14\t10\t0\t6\t2\t0\t9\t1\t0\t1\t0\t0\t7\t5\t2\t0\t0\t1\t0\t0\t0\t2\t14\t4\t7\t6\t2\t0\t0\t1\t0\t9\t0\t2\t9\t0\t6\t1\t0\t7\t10\t2\t0\t1\t0\t6\t2\t2\t16\t0\t0\t0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|
