Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
changeset 8:be0c6b6466cc draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
| author | mvdbeek |
|---|---|
| date | Mon, 19 Sep 2016 06:16:21 -0400 |
| parents | c9e267cb84c0 |
| children | 92898cc3ea19 |
| files | plot_size_readmap.r readmap.py readmap.xml smRtools.py smRtools.pyc test-data/Readmap_dataframe.tab test-data/Readmaps.pdf test-data/Size_distribution.pdf test-data/Size_distribution_and_Readmaps.pdf test-data/Size_distribution_dataframe.tab tool_dependencies.xml |
| diffstat | 11 files changed, 615 insertions(+), 358 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot_size_readmap.r Mon Sep 19 06:16:21 2016 -0400 @@ -0,0 +1,145 @@ +## Setup R error handling to go to stderr +options( show.error.messages=F, + error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +library(RColorBrewer) +library(lattice) +library(latticeExtra) +library(grid) +library(gridExtra) +library(optparse) + +# Parse arguments +option_list <- list( + make_option(c("-r", "--readmap_tab"), type="character", help="Path to file with tabular readmap"), + make_option(c("-s", "--size_distribution_tab"), type="character", help="Path to file with tabular size distribution"), + make_option("--readmap_pdf", type="character", help="Path to file with readmap plot"), + make_option("--size_distribution_pdf", type="character", help="Path to file with size distribution plot"), + make_option("--combi_pdf", type="character", help="Path to file with size distribution and readmap plot"), + make_option("--title", type="character", help="Title for readmaps and size distribution"), + make_option("--xlabel", type="character", help="xlabel for readmaps and size distribution"), + make_option("--ylabel", type="character", help="ylabel for readmaps and size distribution"), + make_option("--yrange", type="integer", help="Y-axis range"), + make_option("--rows_per_page", type="integer", help="rows_per_page") + ) + +parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) +args = parse_args(parser) + +## data frames implementation + +rm=read.delim(args$readmap_tab, header=T, row.names=NULL) +n_samples=length(unique(rm$sample)) +genes=unique(levels(rm$gene)) +per_gene_readmap=lapply(genes, function(x) subset(rm, gene==x)) +n_genes=length(per_gene_readmap) + +size=read.delim(args$size_distribution_tab, header=T, row.names=NULL) +per_gene_size=lapply(genes, function(x) subset(size, gene==x)) + +## end of data frames implementation + +## functions + +plot_readmap=function(df, ...) { +combineLimits(xyplot(count~coord|factor(sample, levels=unique(sample))+reorder(gene, count, function(x) -sum(abs(x))), +data=df, +type='h', +scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)), +xlab=NULL, main=NULL, ylab=NULL, +as.table=T, +origin = 0, +horizontal=FALSE, +group=polarity, +col=c("red","blue"), +par.strip.text = list(cex=0.7), +...)) +} + +plot_size_distribution= function(df, ...) { + smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);} + bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0, + horizontal=FALSE, +group=polarity, +stack=TRUE, + col=c('red', 'blue'), + cex=0.75, + scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ), + prepanel=smR.prepanel, + xlab = NULL, + ylab = NULL, + main = NULL, + as.table=TRUE, + newpage = T, + par.strip.text = list(cex=0.7), + ...) + combineLimits(bc) + } + +## end of functions + +## function parameters' + +par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) ) +par.settings.size=list(layout.heights=list(top.padding=-1, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) ) +par.settings.combination.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-3), strip.background=list(col=c("lightblue","lightgreen")) ) +par.settings.combination.size=list(layout.heights=list(top.padding=-2, bottom.padding=-0.5), strip.background=list(col=c("lightblue", "lightgreen")) ) + +## end of function parameters' + +## GRAPHS + +if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=args$rows_per_page} else { + rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2 } +if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test + + +pdf(file=args$readmap_pdf, paper="special", height=page_height_simple, width=page_width) +for (i in seq(1,n_genes,rows_per_page)) { +start=i +end=i+rows_per_page-1 +if (end>n_genes) {end=n_genes} +if (args$yrange == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { +readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args.yrange, args.yrange) , par.settings=par.settings.readmap)) } +args_list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1, + top=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"), + left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90) + ) + ) +do.call(grid.arrange, args_list) +} +devname=dev.off() + +pdf(file=args$size_distribution_pdf, paper="special", height=page_height_simple, width=page_width) +for (i in seq(1,n_genes,rows_per_page)) { +start=i +end=i+rows_per_page-1 +if (end>n_genes) {end=n_genes} +plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, par.settings=par.settings.size) ) +args_list=c(plot.list, list(nrow=rows_per_page, ncol=1, + top=textGrob("Size distributions (in nucleotides)", gp=gpar(cex=1), just="top"), + left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90) + ) + ) +do.call(grid.arrange, args_list) +} +devname=dev.off() + +pdf(file=args$combi_pdf, paper="special", height=page_height_combi, width=page_width) +if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1} +for (i in seq(1,n_genes,rows_per_page/2)) { +start=i +end=i+rows_per_page/2-1 +if (end>n_genes) {end=n_genes} +if (args$yrange == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { +readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args.yrange, args.yrange), par.settings=par.settings.readmap)) } +size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size)) +plot.list=rbind(readmap_plot.list, size_plot.list ) +args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1, + top=textGrob(args$title, gp=gpar(cex=1), just="top"), + left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90), + sub=textGrob(args$xlabel, gp=gpar(cex=1), just="bottom") + ) + ) +do.call(grid.arrange, args_list) +} +devname=dev.off() \ No newline at end of file
--- a/readmap.py Sun Sep 18 12:55:27 2016 -0400 +++ b/readmap.py Mon Sep 19 06:16:21 2016 -0400 @@ -23,7 +23,6 @@ the_parser.add_argument('--gff', type=str, help="GFF containing regions of interest") the_parser.add_argument('--minquery', type=int, help="Minimum readsize") the_parser.add_argument('--maxquery', type=int, help="Maximum readsize") - the_parser.add_argument('--rcode', type=str, help="R script") args = the_parser.parse_args() return args @@ -38,7 +37,6 @@ size_distribution_file=args.output_size_distribution minquery=args.minquery maxquery=args.maxquery -Rcode = args.rcode filePath=args.input fileExt=args.ext fileLabel=args.label @@ -54,16 +52,19 @@ biosample=fileLabel[i], size_inf=minquery, size_sup=maxquery, norm=norm) return MasterListOfGenomes -def dataframe_sanityzer (listofdatalines): - Dict = defaultdict(float) +def remove_null_entries(listofdatalines): + """ + This function removes genes that have no reads aligned. + """ + Dict = defaultdict(float) for line in listofdatalines: fields= line.split("\t") - Dict[fields[0]] += float (fields[2]) + Dict[fields[0]] += abs(float(fields[2])) filtered_list = [] for line in listofdatalines: fields= line.split("\t") if Dict[fields[0]] != 0: - filtered_list.append(line) + filtered_list.append(line) return filtered_list @@ -110,9 +111,8 @@ plottable = dict[gene].readplot() plottable = handle_start_stop_coordinates(plottable, readDict) for line in plottable: - #print >>readmap, "%s\t%s" % (line, sample) listoflines.append ("%s\t%s" % (line, sample)) - listoflines = dataframe_sanityzer(listoflines) + listoflines = remove_null_entries(listoflines) for line in listoflines: print >>readmap, line @@ -126,19 +126,15 @@ else: dict=readDict[sample].instanceDict for gene in dict.keys(): - histogram = dict[gene].size_histogram(minquery=args.minquery, maxquery=args.maxquery) + histogram = dict[gene].size_histogram(minquery=minquery, maxquery=maxquery) for polarity in histogram.keys(): if polarity=='both': continue - #for size in xrange(args.minquery, args.maxquery): - # if not size in histogram[polarity].keys(): - # histogram[size]=0 for size, count in histogram[polarity].iteritems(): - #print >>size_distrib, "%s\t%s\t%s\t%s\t%s" % (gene, size, count, polarity, sample) # test, changed the order accordingly listoflines.append ("%s\t%s\t%s\t%s\t%s" % (gene, size, count, polarity, sample) ) - listoflines = dataframe_sanityzer(listoflines) + listoflines = remove_null_entries(listoflines) for line in listoflines: - print >>size_distrib, line + print >>size_distrib, line def gff_item_subinstances(readDict, gff3): GFFinstanceDict=OrderedDict() @@ -154,10 +150,6 @@ item_downstream_coordinate = int(gff_fields[4]) item_polarity = gff_fields[6] for sample in readDict.keys(): -## this is not required anymore but test -# if not GFFinstanceDict.has_key(sample): -# GFFinstanceDict[sample]={} -#### subinstance=extractsubinstance(item_upstream_coordinate, item_downstream_coordinate, readDict[sample].instanceDict[chrom]) if item_polarity == '-': subinstance.readDict={key*-1:value for key, value in subinstance.readDict.iteritems()} @@ -172,8 +164,4 @@ write_readplot_dataframe(MasterListOfGenomes, readmap_file) write_size_distribution_dataframe(MasterListOfGenomes, size_distribution_file) - -R_command="Rscript "+ Rcode -process = subprocess.Popen(R_command.split()) -process.wait()
--- a/readmap.xml Sun Sep 18 12:55:27 2016 -0400 +++ b/readmap.xml Mon Sep 19 06:16:21 2016 -0400 @@ -1,239 +1,109 @@ -<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.5"> - <description>from sRbowtie aligment</description> - <requirements> - <requirement type="package" version="0.12.7">bowtie</requirement> - <requirement type="package" version="0.7.7">pysam</requirement> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="package" version="2.14">biocbasics</requirement> - <requirement type="package" version="1.9">numpy</requirement> - </requirements> -<command interpreter="python"> - readmap.py - #if $refGenomeSource.genomeSource == "history": - --reference_fasta ## sys.argv[2] - $refGenomeSource.ownFile ## index source - #else: - #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] - --reference_bowtie_index - $reference - #end if - --rcode - $plotCode - --output_readmap - $readmap_dataframe - --output_size_distribution - $size_distribution_dataframe - --minquery - $minquery - --maxquery - $maxquery - --input - #for $i in $refGenomeSource.series - $i.input - #end for - --ext - #for $i in $refGenomeSource.series - $i.input.ext - #end for - --label - #for $i in $refGenomeSource.series - "$i.input.name" - #end for - --normalization_factor - #for $i in $refGenomeSource.series - $i.norm - #end for - #if $gff: - --gff - $gff - #end if - +<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.2.0"> + <description>from sRbowtie aligment</description> + <requirements> + <requirement type="package" version="1.0.0">bowtie</requirement> + <requirement type="package" version="0.9.0">pysam</requirement> + <requirement type="package" version="1.9.3">numpy</requirement> + <requirement type="package" version="1.3.0">r-optparse</requirement> + <requirement type="package" version="0.6_26">r-latticeextra</requirement> + <requirement type="package" version="2.0.0">r-gridextra</requirement> + </requirements> + <command><![CDATA[ + python2 $__tool_directory__/readmap.py + #if $refGenomeSource.genomeSource == "history": + --reference_fasta + $refGenomeSource.ownFile ## index source + #else: + #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] + --reference_bowtie_index + $reference + #end if + --output_readmap + "$readmap_dataframe" + --output_size_distribution + "$size_distribution_dataframe" + --minquery $minquery + --maxquery $maxquery + --input + #for $i in $refGenomeSource.series + $i.input + #end for + --ext + #for $i in $refGenomeSource.series + $i.input.ext + #end for + --label + #for $i in $refGenomeSource.series + "$i.input.name" + #end for + --normalization_factor + #for $i in $refGenomeSource.series + $i.norm + #end for + #if $gff: + --gff + $gff + #end if + ; Rscript $__tool_directory__/plot_size_readmap.r + --readmap_tab "$readmap_dataframe" + --size_distribution_tab "$size_distribution_dataframe" + --readmap_pdf "$readmap_PDF" + --size_distribution_pdf "$size_PDF" + --combi_pdf "$combi_PDF" + --title "$title" + --xlabel "$xlabel" + --ylabel "$ylabel" + --yrange "$yrange" + --rows_per_page "$rows_per_page" + ]]> </command> - <inputs> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <repeat name="series" title="Add alignment files"> - <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"> - <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> - </param> - <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> - </repeat> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" /> - <repeat name="series" title="Add alignment files"> - <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/> - <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> - </repeat> - </when> - </conditional> - <param name="gff" type="data" format="gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/> - <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> --> - <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/> - <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/> - <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/> - <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/> - <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/> - <param name="yrange" type="integer" size="3" value="0" label="y axis range for readmaps. 0 means auto-scaling."/> - <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?"> - <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/> - </param> - </inputs> - <configfiles> - <configfile name="plotCode"> - ## Setup R error handling to go to stderr - options( show.error.messages=F, - error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) - library(RColorBrewer) - library(lattice) - library(latticeExtra) - library(grid) - library(gridExtra) - - ## data frames implementation - - rm=read.delim("${readmap_dataframe}", header=T, row.names=NULL) - n_samples=length(unique(rm\$sample)) - genes=unique(levels(rm\$gene)) - per_gene_readmap=lapply(genes, function(x) subset(rm, gene==x)) ####### ? - n_genes=length(per_gene_readmap) - - size=read.delim("${size_distribution_dataframe}", header=T, row.names=NULL) - per_gene_size=lapply(genes, function(x) subset(size, gene==x)) ###### ? - - ## end of data frames implementation - - ## functions - - plot_readmap=function(df, ...) { - combineLimits(xyplot(count~coord|factor(sample, levels=unique(sample))+reorder(gene, count, function(x) -sum(abs(x))), - data=df, - type='h', - scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)), - xlab=NULL, main=NULL, ylab=NULL, - as.table=T, - origin = 0, - horizontal=FALSE, - group=polarity, - col=c("red","blue"), - par.strip.text = list(cex=0.7), - ...)) - } - - plot_size_distribution= function(df, ...) { - smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);} - bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0, - horizontal=FALSE, - group=polarity, - stack=TRUE, - col=c('red', 'blue'), - cex=0.75, - scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ), - prepanel=smR.prepanel, - xlab = NULL, - ylab = NULL, - main = NULL, - as.table=TRUE, - newpage = T, - par.strip.text = list(cex=0.7), - ...) - combineLimits(bc) - } - - ## end of functions - - ## function parameters' - - par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) ) - par.settings.size=list(layout.heights=list(top.padding=-1, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) ) - par.settings.combination.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-3), strip.background=list(col=c("lightblue","lightgreen")) ) - par.settings.combination.size=list(layout.heights=list(top.padding=-2, bottom.padding=-0.5), strip.background=list(col=c("lightblue", "lightgreen")) ) - - ## end of function parameters' - - ## GRAPHS - - if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else { - rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2; extrarow=0 } - ## rows_per_page= 8; page_height_simple = 11.69/7*n_genes; page_height_combi=11.69/9*(n_genes*2); extrarow=0 } - ## rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 } - if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test - - pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width) - for (i in seq(1,n_genes,rows_per_page)) { - start=i - end=i+rows_per_page-1 - if (end>n_genes) {end=n_genes} - if (${yrange} == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { - readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}) , par.settings=par.settings.readmap)) } - args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1, - main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"), - left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90) - #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom") - ) - ) - do.call(grid.arrange, args.list) - } - devname=dev.off() - - - pdf(file="${size_PDF}", paper="special", height=page_height_simple, width=page_width) - for (i in seq(1,n_genes,rows_per_page)) { - start=i - end=i+rows_per_page-1 - if (end>n_genes) {end=n_genes} - plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, par.settings=par.settings.size) ) - args.list=c(plot.list, list(nrow=rows_per_page, ncol=1, - main=textGrob("Size distributions (in nucleotides)", gp=gpar(cex=1), just="top"), - left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90) - #sub="readsize in nucleotides" - ) - ) - do.call(grid.arrange, args.list) - } - devname=dev.off() - - pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width) - if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1} - for (i in seq(1,n_genes,rows_per_page/2)) { - start=i - end=i+rows_per_page/2-1 - if (end>n_genes) {end=n_genes} - if (${yrange} == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { - readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}), par.settings=par.settings.readmap)) } - size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size)) - plot.list=rbind(readmap_plot.list, size_plot.list ) - args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1, - main=textGrob("${title}", gp=gpar(cex=1), just="top"), - left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90), - sub=textGrob("${xlabel}", gp=gpar(cex=1), just="bottom") - ) - ) - do.call(grid.arrange, args.list) - } - devname=dev.off() - - - </configfile> - </configfiles> - - <outputs> - <data format="tabular" name="readmap_dataframe" label="Readmap dataframe"/> - <data format="tabular" name="size_distribution_dataframe" label="Size distribution dataframe"/> - <data format="pdf" name="readmap_PDF" label="Readmaps"/> - <data format="pdf" name="size_PDF" label="Size distribution"/> - <data format="pdf" name="combi_PDF" label="Size distribution and Readmaps"/> - </outputs> -<help> + <inputs> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <repeat name="series" title="Add alignment files"> + <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"> + <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> + </param> + <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> + </repeat> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" /> + <repeat name="series" title="Add alignment files"> + <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/> + <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> + </repeat> + </when> + </conditional> + <param name="gff" type="data" format="gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/> + <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> --> + <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/> + <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/> + <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/> + <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/> + <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/> + <param name="yrange" type="integer" size="3" value="0" label="y axis range for readmaps. 0 means auto-scaling."/> + <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?"> + <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/> + </param> + </inputs> + <outputs> + <data format="tabular" name="readmap_dataframe" label="Readmap dataframe"/> + <data format="tabular" name="size_distribution_dataframe" label="Size distribution dataframe"/> + <data format="pdf" name="readmap_PDF" label="Readmaps"/> + <data format="pdf" name="size_PDF" label="Size distribution"/> + <data format="pdf" name="combi_PDF" label="Size distribution and Readmaps"/> + </outputs> + <help> **What it does** -Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a "Readmap", -where by default for each "chromosome" the position of the read is recorded on the x-axis, and the y-axis indicates +Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a "Readmap", +where by default for each "chromosome" the position of the read is recorded on the x-axis, and the y-axis indicates the number of reads per position. Reads that map in sense are on the top, reads that map antisense are on the bottom. @@ -248,42 +118,39 @@ Query sequence:: For a SAM file as the following: - 5 16 2L_79 24393 255 17M * 0 0 CCTTCATCTTTTTTTTT IIIIIIIIIIIIIIIII XA:i:0 MD:Z:17 NM:i:0 +5 16 2L_79 24393 255 17M * 0 0 CCTTCATCTTTTTTTTT IIIIIIIIIIIIIIIII XA:i:0 MD:Z:17 NM:i:0 - 11 0 2R_1 12675 255 21M * 0 0 AAAAAAAACGCGTCCTTGTGC IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0 +11 0 2R_1 12675 255 21M * 0 0 AAAAAAAACGCGTCCTTGTGC IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0 - 2 16 2L_5 669 255 23M * 0 0 TGTTGCTGCATTTCTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0 +2 16 2L_5 669 255 23M * 0 0 TGTTGCTGCATTTCTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0 produce a plot like this: ---- -.. image:: static/images/readmap.png - :height: 800 - :width: 500 +.. image:: static/images/readmap.png +:height: 800 +:width: 500 -</help> - <tests> - <test> - <param name="genomeSource" value="history" /> - <param name="ownFile" value ="transposons.fasta" ftype="fasta" /> - <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/> - <param name="series_0|norm" value="1" /> - <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/> - <param name="series_1|norm" value="1" /> - <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/> - <param name="series_2|norm" value="1" /> - <param name="minquery" value="20" /> - <param name="maxquery" value="30" /> - <param name="title" value="Readmaps and size distributions" /> - <param name="xlabel" value="Coordinates/read size" /> - <param name="ylabel" value="Number of reads" /> - <param name="rows_per_page" value="8" /> - <output name="readmap_dataframe" ftype="tabular" file="Readmap_dataframe.tab" /> - <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" /> - <output name="readmap_PDF" ftype="pdf" file="Readmaps.pdf" /> - <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" /> - <output name="combi_PDF" ftype="pdf" file="Size_distribution_and_Readmaps.pdf" /> - </test> - </tests> + </help> + <tests> + <test> + <param name="genomeSource" value="history" /> + <param name="ownFile" value ="transposons.fasta" ftype="fasta" /> + <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/> + <param name="series_0|norm" value="1" /> + <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/> + <param name="series_1|norm" value="1" /> + <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/> + <param name="series_2|norm" value="1" /> + <param name="minquery" value="20" /> + <param name="maxquery" value="30" /> + <param name="title" value="Readmaps and size distributions" /> + <param name="xlabel" value="Coordinates/read size" /> + <param name="ylabel" value="Number of reads" /> + <param name="rows_per_page" value="8" /> + <output name="readmap_dataframe" ftype="tabular" file="Readmap_dataframe.tab" /> + <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" /> + </test> + </tests> </tool>
--- a/smRtools.py Sun Sep 18 12:55:27 2016 -0400 +++ b/smRtools.py Mon Sep 19 06:16:21 2016 -0400 @@ -142,26 +142,6 @@ self.alignedReads += 1 F.close() return self.instanceDict -# elif self.alignmentFileFormat == "sam": -# F = open (self.alignmentFile, "r") -# dict = {"0":"+", "16":"-"} -# for line in F: -# if line[0]=='@': -# continue -# fields = line.split() -# if fields[2] == "*": continue -# polarity = dict[fields[1]] -# gene = fields[2] -# offset = int(fields[3]) -# size = len (fields[9]) -# if self.size_inf: -# if (size>=self.size_inf and size<= self.size_sup): -# self.instanceDict[gene].addread (polarity, offset, size) -# self.alignedReads += 1 -# else: -# self.instanceDict[gene].addread (polarity, offset, size) -# self.alignedReads += 1 -# F.close() elif self.alignmentFileFormat == "bam" or self.alignmentFileFormat == "sam": import pysam samfile = pysam.Samfile(self.alignmentFile) @@ -184,22 +164,6 @@ self.alignedReads += 1 return self.instanceDict -# def size_histogram (self): -# size_dict={} -# size_dict['F']= defaultdict (int) -# size_dict['R']= defaultdict (int) -# size_dict['both'] = defaultdict (int) -# for item in self.instanceDict: -# buffer_dict_F = self.instanceDict[item].size_histogram()['F'] -# buffer_dict_R = self.instanceDict[item].size_histogram()['R'] -# for size in buffer_dict_F: -# size_dict['F'][size] += buffer_dict_F[size] -# for size in buffer_dict_R: -# size_dict['R'][size] -= buffer_dict_R[size] -# allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) ) -# for size in allSizeKeys: -# size_dict['both'][size] = size_dict['F'][size] + size_dict['R'][size] -# return size_dict def size_histogram (self): # in HandleSmRNAwindows '''refactored on 7-9-2014 to debug size_histogram tool''' size_dict={} @@ -361,24 +325,7 @@ for offset in range (min(dicsize.keys()), max(dicsize.keys())+1): dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values return dicsize - -# def size_histogram(self): -# norm=self.norm -# hist_dict={} -# hist_dict['F']={} -# hist_dict['R']={} -# for offset in self.readDict: -# for size in self.readDict[offset]: -# if offset < 0: -# hist_dict['R'][size] = hist_dict['R'].get(size, 0) - 1*norm -# else: -# hist_dict['F'][size] = hist_dict['F'].get(size, 0) + 1*norm -# ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate ! -# if not (hist_dict['F']) and (not hist_dict['R']): -# hist_dict['F'][21] = 0 -# hist_dict['R'][21] = 0 -# ## -# return hist_dict + def size_histogram(self, minquery=None, maxquery=None): # in SmRNAwindow '''refactored on 7-9-2014 to debug size_histogram tool''' @@ -480,7 +427,6 @@ return ". | %s" % (freqDic["Trev"] / reverse_sum * 100) else: return "%s | %s" % (freqDic["Tfor"] / forward_sum * 100, freqDic["Trev"] / reverse_sum * 100) - def readplot (self): norm=self.norm
--- a/test-data/Readmap_dataframe.tab Sun Sep 18 12:55:27 2016 -0400 +++ b/test-data/Readmap_dataframe.tab Mon Sep 19 06:16:21 2016 -0400 @@ -1,4 +1,5 @@ gene coord count polarity sample +FBti0020401 0 0 F sample1.srbowtie_out FBti0020401 78 -1.0 R sample1.srbowtie_out FBti0020401 102 -1.0 R sample1.srbowtie_out FBti0020401 271 -1.0 R sample1.srbowtie_out @@ -47,12 +48,20 @@ FBti0020401 6184 -2.0 R sample1.srbowtie_out FBti0020401 6209 1.0 F sample1.srbowtie_out FBti0020401 6327 -2.0 R sample1.srbowtie_out +FBti0020401 6348 0 F sample1.srbowtie_out +FBti0020406 0 0 F sample1.srbowtie_out FBti0020406 174 1.0 F sample1.srbowtie_out FBti0020406 516 -1.0 R sample1.srbowtie_out FBti0020406 542 -1.0 R sample1.srbowtie_out FBti0020406 595 -1.0 R sample1.srbowtie_out +FBti0020406 812 0 F sample1.srbowtie_out +FBti0019511 0 0 F sample1.srbowtie_out FBti0019511 1 0 F sample1.srbowtie_out +FBti0019511 1402 0 F sample1.srbowtie_out +FBti0019512 0 0 F sample1.srbowtie_out FBti0019512 1 0 F sample1.srbowtie_out +FBti0019512 221 0 F sample1.srbowtie_out +FBti0019473 0 0 F sample1.srbowtie_out FBti0019473 62 -1.0 R sample1.srbowtie_out FBti0019473 199 -1.0 R sample1.srbowtie_out FBti0019473 203 1.0 F sample1.srbowtie_out @@ -109,6 +118,8 @@ FBti0019473 4860 -1.0 R sample1.srbowtie_out FBti0019473 4939 1.0 F sample1.srbowtie_out FBti0019473 4948 -2.0 R sample1.srbowtie_out +FBti0019473 5368 0 F sample1.srbowtie_out +FBti0019518 0 0 F sample1.srbowtie_out FBti0019518 130 1.0 F sample1.srbowtie_out FBti0019518 182 1.0 F sample1.srbowtie_out FBti0019518 217 -1.0 R sample1.srbowtie_out @@ -117,6 +128,8 @@ FBti0019518 589 -1.0 R sample1.srbowtie_out FBti0019518 617 3.0 F sample1.srbowtie_out FBti0019518 817 -1.0 R sample1.srbowtie_out +FBti0019518 1012 0 F sample1.srbowtie_out +FBti0019519 0 0 F sample1.srbowtie_out FBti0019519 1202 2.0 F sample1.srbowtie_out FBti0019519 1325 2.0 F sample1.srbowtie_out FBti0019519 1379 1.0 F sample1.srbowtie_out @@ -132,7 +145,11 @@ FBti0019519 1985 2.0 F sample1.srbowtie_out FBti0019519 2059 1.0 F sample1.srbowtie_out FBti0019519 2247 1.0 F sample1.srbowtie_out +FBti0019519 3897 0 F sample1.srbowtie_out +FBti0019514 0 0 F sample1.srbowtie_out FBti0019514 337 1.0 F sample1.srbowtie_out +FBti0019514 466 0 F sample1.srbowtie_out +FBti0019515 0 0 F sample1.srbowtie_out FBti0019515 531 -1.0 R sample1.srbowtie_out FBti0019515 1099 -1.0 R sample1.srbowtie_out FBti0019515 1113 1.0 F sample1.srbowtie_out @@ -154,11 +171,15 @@ FBti0019515 2475 -8.0 R sample1.srbowtie_out FBti0019515 2484 -1.0 R sample1.srbowtie_out FBti0019515 2520 1.0 F sample1.srbowtie_out +FBti0019515 2592 0 F sample1.srbowtie_out +FBti0019516 0 0 F sample1.srbowtie_out FBti0019516 15 1.0 F sample1.srbowtie_out FBti0019516 264 1.0 F sample1.srbowtie_out FBti0019516 737 5.0 F sample1.srbowtie_out FBti0019516 799 1.0 F sample1.srbowtie_out FBti0019516 941 -1.0 R sample1.srbowtie_out +FBti0019516 1132 0 F sample1.srbowtie_out +FBti0019517 0 0 F sample1.srbowtie_out FBti0019517 5 1.0 F sample1.srbowtie_out FBti0019517 47 -1.0 R sample1.srbowtie_out FBti0019517 138 -1.0 R sample1.srbowtie_out @@ -184,6 +205,8 @@ FBti0019517 515 -1.0 R sample1.srbowtie_out FBti0019517 581 1.0 F sample1.srbowtie_out FBti0019517 590 -1.0 R sample1.srbowtie_out +FBti0019517 740 0 F sample1.srbowtie_out +FBti0020404 0 0 F sample1.srbowtie_out FBti0020404 40 1.0 F sample1.srbowtie_out FBti0020404 56 1.0 F sample1.srbowtie_out FBti0020404 210 3.0 F sample1.srbowtie_out @@ -195,10 +218,14 @@ FBti0020404 835 -3.0 R sample1.srbowtie_out FBti0020404 1309 -2.0 R sample1.srbowtie_out FBti0020404 1383 -1.0 R sample1.srbowtie_out +FBti0020404 1470 0 F sample1.srbowtie_out +FBti0020405 0 0 F sample1.srbowtie_out FBti0020405 127 -1.0 R sample1.srbowtie_out FBti0020405 404 1.0 F sample1.srbowtie_out FBti0020405 586 2.0 F sample1.srbowtie_out FBti0020405 674 1.0 F sample1.srbowtie_out +FBti0020405 745 0 F sample1.srbowtie_out +FBti0019499 0 0 F sample1.srbowtie_out FBti0019499 18 1.0 F sample1.srbowtie_out FBti0019499 271 1.0 F sample1.srbowtie_out FBti0019499 369 -1.0 R sample1.srbowtie_out @@ -233,9 +260,15 @@ FBti0019499 1565 -5.0 R sample1.srbowtie_out FBti0019499 1606 -1.0 R sample1.srbowtie_out FBti0019499 1641 -1.0 R sample1.srbowtie_out +FBti0019499 1728 0 F sample1.srbowtie_out +FBti0019472 0 0 F sample1.srbowtie_out FBti0019472 210 2.0 F sample1.srbowtie_out FBti0019472 691 2.0 F sample1.srbowtie_out +FBti0019472 1044 0 F sample1.srbowtie_out +FBti0020396 0 0 F sample1.srbowtie_out FBti0020396 1 0 F sample1.srbowtie_out +FBti0020396 1838 0 F sample1.srbowtie_out +FBti0019476 0 0 F sample1.srbowtie_out FBti0019476 25 -1.0 R sample1.srbowtie_out FBti0019476 533 -1.0 R sample1.srbowtie_out FBti0019476 781 1.0 F sample1.srbowtie_out @@ -252,6 +285,8 @@ FBti0019476 3155 -8.0 R sample1.srbowtie_out FBti0019476 3156 -1.0 R sample1.srbowtie_out FBti0019476 3589 -1.0 R sample1.srbowtie_out +FBti0019476 4183 0 F sample1.srbowtie_out +FBti0019493 0 0 F sample1.srbowtie_out FBti0019493 37 1.0 F sample1.srbowtie_out FBti0019493 149 -1.0 R sample1.srbowtie_out FBti0019493 153 -1.0 R sample1.srbowtie_out @@ -532,6 +567,8 @@ FBti0019493 4386 1.0 F sample1.srbowtie_out FBti0019493 4388 1.0 F sample1.srbowtie_out FBti0019493 4398 -1.0 R sample1.srbowtie_out +FBti0019493 4431 0 F sample1.srbowtie_out +FBti0019492 0 0 F sample1.srbowtie_out FBti0019492 14 1.0 F sample1.srbowtie_out FBti0019492 31 -1.0 R sample1.srbowtie_out FBti0019492 40 -1.0 R sample1.srbowtie_out @@ -540,6 +577,8 @@ FBti0019492 549 -1.0 R sample1.srbowtie_out FBti0019492 554 -1.0 R sample1.srbowtie_out FBti0019492 874 -1.0 R sample1.srbowtie_out +FBti0019492 1035 0 F sample1.srbowtie_out +FBti0019495 0 0 F sample1.srbowtie_out FBti0019495 159 -1.0 R sample1.srbowtie_out FBti0019495 197 -1.0 R sample1.srbowtie_out FBti0019495 273 -1.0 R sample1.srbowtie_out @@ -592,10 +631,14 @@ FBti0019495 8015 1.0 F sample1.srbowtie_out FBti0019495 8462 -1.0 R sample1.srbowtie_out FBti0019495 8487 -1.0 R sample1.srbowtie_out +FBti0019495 8526 0 F sample1.srbowtie_out +FBti0019494 0 0 F sample1.srbowtie_out FBti0019494 210 1.0 F sample1.srbowtie_out FBti0019494 561 1.0 F sample1.srbowtie_out FBti0019494 648 1.0 F sample1.srbowtie_out FBti0019494 689 1.0 F sample1.srbowtie_out +FBti0019494 1060 0 F sample1.srbowtie_out +FBti0020395 0 0 F sample1.srbowtie_out FBti0020395 207 1.0 F sample1.srbowtie_out FBti0020395 370 -1.0 R sample1.srbowtie_out FBti0020395 418 2.0 F sample1.srbowtie_out @@ -614,6 +657,8 @@ FBti0020395 987 1.0 F sample1.srbowtie_out FBti0020395 988 1.0 F sample1.srbowtie_out FBti0020395 1049 -1.0 R sample1.srbowtie_out +FBti0020395 1082 0 F sample1.srbowtie_out +FBti0019483 0 0 F sample1.srbowtie_out FBti0019483 38 -1.0 R sample1.srbowtie_out FBti0019483 42 -1.0 R sample1.srbowtie_out FBti0019483 44 -1.0 R sample1.srbowtie_out @@ -626,6 +671,8 @@ FBti0019483 440 -1.0 R sample1.srbowtie_out FBti0019483 542 1.0 F sample1.srbowtie_out FBti0019483 589 1.0 F sample1.srbowtie_out +FBti0019483 661 0 F sample1.srbowtie_out +FBti0020398 0 0 F sample1.srbowtie_out FBti0020398 74 1.0 F sample1.srbowtie_out FBti0020398 114 3.0 F sample1.srbowtie_out FBti0020398 139 1.0 F sample1.srbowtie_out @@ -636,6 +683,8 @@ FBti0020398 417 1.0 F sample1.srbowtie_out FBti0020398 456 2.0 F sample1.srbowtie_out FBti0020398 474 -1.0 R sample1.srbowtie_out +FBti0020398 565 0 F sample1.srbowtie_out +FBti0019509 0 0 F sample1.srbowtie_out FBti0019509 76 -3.0 R sample1.srbowtie_out FBti0019509 78 -1.0 R sample1.srbowtie_out FBti0019509 104 -2.0 R sample1.srbowtie_out @@ -657,6 +706,8 @@ FBti0019509 1136 1.0 F sample1.srbowtie_out FBti0019509 1143 3.0 F sample1.srbowtie_out FBti0019509 1152 -1.0 R sample1.srbowtie_out +FBti0019509 1209 0 F sample1.srbowtie_out +FBti0019507 0 0 F sample1.srbowtie_out FBti0019507 56 1.0 F sample1.srbowtie_out FBti0019507 82 1.0 F sample1.srbowtie_out FBti0019507 101 1.0 F sample1.srbowtie_out @@ -670,6 +721,8 @@ FBti0019507 810 1.0 F sample1.srbowtie_out FBti0019507 902 -1.0 R sample1.srbowtie_out FBti0019507 967 1.0 F sample1.srbowtie_out +FBti0019507 1039 0 F sample1.srbowtie_out +FBti0019504 0 0 F sample1.srbowtie_out FBti0019504 74 -1.0 R sample1.srbowtie_out FBti0019504 84 1.0 F sample1.srbowtie_out FBti0019504 94 1.0 F sample1.srbowtie_out @@ -699,6 +752,8 @@ FBti0019504 2994 -1.0 R sample1.srbowtie_out FBti0019504 3008 1.0 F sample1.srbowtie_out FBti0019504 3027 -1.0 R sample1.srbowtie_out +FBti0019504 3082 0 F sample1.srbowtie_out +FBti0019503 0 0 F sample1.srbowtie_out FBti0019503 40 1.0 F sample1.srbowtie_out FBti0019503 75 1.0 F sample1.srbowtie_out FBti0019503 78 -1.0 R sample1.srbowtie_out @@ -717,6 +772,8 @@ FBti0019503 327 -1.0 R sample1.srbowtie_out FBti0019503 333 2.0 F sample1.srbowtie_out FBti0019503 342 -1.0 R sample1.srbowtie_out +FBti0019503 422 0 F sample1.srbowtie_out +FBti0019502 0 0 F sample1.srbowtie_out FBti0019502 42 1.0 F sample1.srbowtie_out FBti0019502 306 1.0 F sample1.srbowtie_out FBti0019502 380 1.0 F sample1.srbowtie_out @@ -726,7 +783,11 @@ FBti0019502 884 -2.0 R sample1.srbowtie_out FBti0019502 916 -1.0 R sample1.srbowtie_out FBti0019502 990 -3.0 R sample1.srbowtie_out +FBti0019502 1076 0 F sample1.srbowtie_out +FBti0019501 0 0 F sample1.srbowtie_out FBti0019501 384 1.0 F sample1.srbowtie_out +FBti0019501 966 0 F sample1.srbowtie_out +FBti0019500 0 0 F sample1.srbowtie_out FBti0019500 56 1.0 F sample1.srbowtie_out FBti0019500 91 1.0 F sample1.srbowtie_out FBti0019500 102 1.0 F sample1.srbowtie_out @@ -736,6 +797,8 @@ FBti0019500 728 3.0 F sample1.srbowtie_out FBti0019500 918 -1.0 R sample1.srbowtie_out FBti0019500 1024 -1.0 R sample1.srbowtie_out +FBti0019500 1111 0 F sample1.srbowtie_out +FBti0020402 0 0 F sample1.srbowtie_out FBti0020402 172 -1.0 R sample1.srbowtie_out FBti0020402 173 -1.0 R sample1.srbowtie_out FBti0020402 320 -1.0 R sample1.srbowtie_out @@ -790,6 +853,8 @@ FBti0020402 5930 -1.0 R sample1.srbowtie_out FBti0020402 5984 -2.0 R sample1.srbowtie_out FBti0020402 6112 1.0 F sample1.srbowtie_out +FBti0020402 6438 0 F sample1.srbowtie_out +FBti0020410 0 0 F sample1.srbowtie_out FBti0020410 43 -1.0 R sample1.srbowtie_out FBti0020410 107 -1.0 R sample1.srbowtie_out FBti0020410 676 -1.0 R sample1.srbowtie_out @@ -848,6 +913,8 @@ FBti0020410 6285 1.0 F sample1.srbowtie_out FBti0020410 6303 -1.0 R sample1.srbowtie_out FBti0020410 6480 -1.0 R sample1.srbowtie_out +FBti0020410 6752 0 F sample1.srbowtie_out +FBti0020403 0 0 F sample1.srbowtie_out FBti0020403 40 1.0 F sample1.srbowtie_out FBti0020403 57 1.0 F sample1.srbowtie_out FBti0020403 161 1.0 F sample1.srbowtie_out @@ -855,12 +922,18 @@ FBti0020403 731 -1.0 R sample1.srbowtie_out FBti0020403 860 -1.0 R sample1.srbowtie_out FBti0020403 908 -1.0 R sample1.srbowtie_out +FBti0020403 1101 0 F sample1.srbowtie_out +FBti0019486 0 0 F sample1.srbowtie_out FBti0019486 286 1.0 F sample1.srbowtie_out FBti0019486 378 1.0 F sample1.srbowtie_out FBti0019486 498 2.0 F sample1.srbowtie_out FBti0019486 778 -1.0 R sample1.srbowtie_out FBti0019486 1198 -1.0 R sample1.srbowtie_out +FBti0019486 1205 0 F sample1.srbowtie_out +FBti0019489 0 0 F sample1.srbowtie_out FBti0019489 1 0 F sample1.srbowtie_out +FBti0019489 369 0 F sample1.srbowtie_out +FBti0019484 0 0 F sample1.srbowtie_out FBti0019484 210 1.0 F sample1.srbowtie_out FBti0019484 264 2.0 F sample1.srbowtie_out FBti0019484 312 1.0 F sample1.srbowtie_out @@ -870,9 +943,15 @@ FBti0019484 905 -1.0 R sample1.srbowtie_out FBti0019484 952 1.0 F sample1.srbowtie_out FBti0019484 961 -1.0 R sample1.srbowtie_out +FBti0019484 1084 0 F sample1.srbowtie_out +FBti0019485 0 0 F sample1.srbowtie_out FBti0019485 168 1.0 F sample1.srbowtie_out FBti0019485 519 1.0 F sample1.srbowtie_out +FBti0019485 1075 0 F sample1.srbowtie_out +FBti0019482 0 0 F sample1.srbowtie_out FBti0019482 112 -1.0 R sample1.srbowtie_out +FBti0019482 597 0 F sample1.srbowtie_out +FBti0020400 0 0 F sample1.srbowtie_out FBti0020400 41 1.0 F sample1.srbowtie_out FBti0020400 146 1.0 F sample1.srbowtie_out FBti0020400 205 1.0 F sample1.srbowtie_out @@ -1187,6 +1266,14 @@ FBti0020400 8704 15.0 F sample1.srbowtie_out FBti0020400 8755 1.0 F sample1.srbowtie_out FBti0020400 8849 3.0 F sample1.srbowtie_out +FBti0020400 9398 0 F sample1.srbowtie_out +FBti0019480 0 0 F sample1.srbowtie_out +FBti0019480 417 2.0 F sample1.srbowtie_out +FBti0019480 503 -3.0 R sample1.srbowtie_out +FBti0019480 619 1.0 F sample1.srbowtie_out +FBti0019480 634 -1.0 R sample1.srbowtie_out +FBti0019480 669 0 F sample1.srbowtie_out +FBti0020401 0 0 F sample2.srbowtie_out FBti0020401 142 -1.0 R sample2.srbowtie_out FBti0020401 160 1.0 F sample2.srbowtie_out FBti0020401 250 1.0 F sample2.srbowtie_out @@ -1236,13 +1323,21 @@ FBti0020401 6184 -3.0 R sample2.srbowtie_out FBti0020401 6189 -1.0 R sample2.srbowtie_out FBti0020401 6218 2.0 F sample2.srbowtie_out +FBti0020401 6348 0 F sample2.srbowtie_out +FBti0020406 0 0 F sample2.srbowtie_out FBti0020406 123 -1.0 R sample2.srbowtie_out FBti0020406 497 1.0 F sample2.srbowtie_out FBti0020406 542 -1.0 R sample2.srbowtie_out FBti0020406 543 -2.0 R sample2.srbowtie_out FBti0020406 617 -1.0 R sample2.srbowtie_out +FBti0020406 812 0 F sample2.srbowtie_out +FBti0019511 0 0 F sample2.srbowtie_out FBti0019511 47 -1.0 R sample2.srbowtie_out +FBti0019511 1402 0 F sample2.srbowtie_out +FBti0019512 0 0 F sample2.srbowtie_out FBti0019512 217 -1.0 R sample2.srbowtie_out +FBti0019512 221 0 F sample2.srbowtie_out +FBti0019473 0 0 F sample2.srbowtie_out FBti0019473 153 1.0 F sample2.srbowtie_out FBti0019473 303 1.0 F sample2.srbowtie_out FBti0019473 330 1.0 F sample2.srbowtie_out @@ -1303,11 +1398,15 @@ FBti0019473 4924 -1.0 R sample2.srbowtie_out FBti0019473 5278 -1.0 R sample2.srbowtie_out FBti0019473 5344 -1.0 R sample2.srbowtie_out +FBti0019473 5368 0 F sample2.srbowtie_out +FBti0019518 0 0 F sample2.srbowtie_out FBti0019518 417 1.0 F sample2.srbowtie_out FBti0019518 580 1.0 F sample2.srbowtie_out FBti0019518 617 3.0 F sample2.srbowtie_out FBti0019518 817 -1.0 R sample2.srbowtie_out FBti0019518 819 -1.0 R sample2.srbowtie_out +FBti0019518 1012 0 F sample2.srbowtie_out +FBti0019519 0 0 F sample2.srbowtie_out FBti0019519 1211 -3.0 R sample2.srbowtie_out FBti0019519 1283 -1.0 R sample2.srbowtie_out FBti0019519 1284 -1.0 R sample2.srbowtie_out @@ -1320,8 +1419,12 @@ FBti0019519 1917 -1.0 R sample2.srbowtie_out FBti0019519 1983 3.0 F sample2.srbowtie_out FBti0019519 1985 2.0 F sample2.srbowtie_out +FBti0019519 3897 0 F sample2.srbowtie_out +FBti0019514 0 0 F sample2.srbowtie_out FBti0019514 76 1.0 F sample2.srbowtie_out FBti0019514 342 1.0 F sample2.srbowtie_out +FBti0019514 466 0 F sample2.srbowtie_out +FBti0019515 0 0 F sample2.srbowtie_out FBti0019515 47 -1.0 R sample2.srbowtie_out FBti0019515 240 -1.0 R sample2.srbowtie_out FBti0019515 531 -1.0 R sample2.srbowtie_out @@ -1342,6 +1445,8 @@ FBti0019515 2302 1.0 F sample2.srbowtie_out FBti0019515 2313 -1.0 R sample2.srbowtie_out FBti0019515 2475 -6.0 R sample2.srbowtie_out +FBti0019515 2592 0 F sample2.srbowtie_out +FBti0019516 0 0 F sample2.srbowtie_out FBti0019516 57 -1.0 R sample2.srbowtie_out FBti0019516 264 3.0 F sample2.srbowtie_out FBti0019516 713 1.0 F sample2.srbowtie_out @@ -1349,6 +1454,8 @@ FBti0019516 995 -1.0 R sample2.srbowtie_out FBti0019516 1126 -1.0 R sample2.srbowtie_out FBti0019516 1130 -1.0 R sample2.srbowtie_out +FBti0019516 1132 0 F sample2.srbowtie_out +FBti0019517 0 0 F sample2.srbowtie_out FBti0019517 55 1.0 F sample2.srbowtie_out FBti0019517 92 1.0 F sample2.srbowtie_out FBti0019517 94 1.0 F sample2.srbowtie_out @@ -1371,6 +1478,8 @@ FBti0019517 590 -1.0 R sample2.srbowtie_out FBti0019517 593 -1.0 R sample2.srbowtie_out FBti0019517 617 -1.0 R sample2.srbowtie_out +FBti0019517 740 0 F sample2.srbowtie_out +FBti0020404 0 0 F sample2.srbowtie_out FBti0020404 15 1.0 F sample2.srbowtie_out FBti0020404 43 1.0 F sample2.srbowtie_out FBti0020404 53 -1.0 R sample2.srbowtie_out @@ -1389,7 +1498,11 @@ FBti0020404 948 1.0 F sample2.srbowtie_out FBti0020404 1039 1.0 F sample2.srbowtie_out FBti0020404 1378 1.0 F sample2.srbowtie_out +FBti0020404 1470 0 F sample2.srbowtie_out +FBti0020405 0 0 F sample2.srbowtie_out FBti0020405 262 -1.0 R sample2.srbowtie_out +FBti0020405 745 0 F sample2.srbowtie_out +FBti0019499 0 0 F sample2.srbowtie_out FBti0019499 137 -1.0 R sample2.srbowtie_out FBti0019499 148 -1.0 R sample2.srbowtie_out FBti0019499 193 1.0 F sample2.srbowtie_out @@ -1434,6 +1547,8 @@ FBti0019499 1564 -1.0 R sample2.srbowtie_out FBti0019499 1605 1.0 F sample2.srbowtie_out FBti0019499 1684 1.0 F sample2.srbowtie_out +FBti0019499 1728 0 F sample2.srbowtie_out +FBti0019472 0 0 F sample2.srbowtie_out FBti0019472 130 1.0 F sample2.srbowtie_out FBti0019472 210 2.0 F sample2.srbowtie_out FBti0019472 305 -2.0 R sample2.srbowtie_out @@ -1442,7 +1557,11 @@ FBti0019472 883 1.0 F sample2.srbowtie_out FBti0019472 955 -2.0 R sample2.srbowtie_out FBti0019472 970 1.0 F sample2.srbowtie_out +FBti0019472 1044 0 F sample2.srbowtie_out +FBti0020396 0 0 F sample2.srbowtie_out FBti0020396 1 0 F sample2.srbowtie_out +FBti0020396 1838 0 F sample2.srbowtie_out +FBti0019476 0 0 F sample2.srbowtie_out FBti0019476 423 1.0 F sample2.srbowtie_out FBti0019476 570 -1.0 R sample2.srbowtie_out FBti0019476 733 -1.0 R sample2.srbowtie_out @@ -1460,6 +1579,8 @@ FBti0019476 3158 -1.0 R sample2.srbowtie_out FBti0019476 3310 1.0 F sample2.srbowtie_out FBti0019476 3589 -2.0 R sample2.srbowtie_out +FBti0019476 4183 0 F sample2.srbowtie_out +FBti0019493 0 0 F sample2.srbowtie_out FBti0019493 37 2.0 F sample2.srbowtie_out FBti0019493 51 1.0 F sample2.srbowtie_out FBti0019493 130 -1.0 R sample2.srbowtie_out @@ -1733,12 +1854,16 @@ FBti0019493 4401 -1.0 R sample2.srbowtie_out FBti0019493 4429 -1.0 R sample2.srbowtie_out FBti0019493 4430 -2.0 R sample2.srbowtie_out +FBti0019493 4431 0 F sample2.srbowtie_out +FBti0019492 0 0 F sample2.srbowtie_out FBti0019492 31 -1.0 R sample2.srbowtie_out FBti0019492 206 -1.0 R sample2.srbowtie_out FBti0019492 340 1.0 F sample2.srbowtie_out FBti0019492 394 1.0 F sample2.srbowtie_out FBti0019492 425 -1.0 R sample2.srbowtie_out FBti0019492 551 -1.0 R sample2.srbowtie_out +FBti0019492 1035 0 F sample2.srbowtie_out +FBti0019495 0 0 F sample2.srbowtie_out FBti0019495 384 -1.0 R sample2.srbowtie_out FBti0019495 403 1.0 F sample2.srbowtie_out FBti0019495 505 1.0 F sample2.srbowtie_out @@ -1773,6 +1898,8 @@ FBti0019495 8404 1.0 F sample2.srbowtie_out FBti0019495 8461 -1.0 R sample2.srbowtie_out FBti0019495 8523 -1.0 R sample2.srbowtie_out +FBti0019495 8526 0 F sample2.srbowtie_out +FBti0019494 0 0 F sample2.srbowtie_out FBti0019494 161 1.0 F sample2.srbowtie_out FBti0019494 264 1.0 F sample2.srbowtie_out FBti0019494 309 1.0 F sample2.srbowtie_out @@ -1780,6 +1907,8 @@ FBti0019494 540 -1.0 R sample2.srbowtie_out FBti0019494 564 1.0 F sample2.srbowtie_out FBti0019494 689 4.0 F sample2.srbowtie_out +FBti0019494 1060 0 F sample2.srbowtie_out +FBti0020395 0 0 F sample2.srbowtie_out FBti0020395 168 -1.0 R sample2.srbowtie_out FBti0020395 418 1.0 F sample2.srbowtie_out FBti0020395 427 -1.0 R sample2.srbowtie_out @@ -1799,6 +1928,8 @@ FBti0020395 1045 -1.0 R sample2.srbowtie_out FBti0020395 1049 -2.0 R sample2.srbowtie_out FBti0020395 1054 -1.0 R sample2.srbowtie_out +FBti0020395 1082 0 F sample2.srbowtie_out +FBti0019483 0 0 F sample2.srbowtie_out FBti0019483 29 -1.0 R sample2.srbowtie_out FBti0019483 74 -1.0 R sample2.srbowtie_out FBti0019483 99 -1.0 R sample2.srbowtie_out @@ -1808,6 +1939,8 @@ FBti0019483 377 1.0 F sample2.srbowtie_out FBti0019483 405 -1.0 R sample2.srbowtie_out FBti0019483 594 1.0 F sample2.srbowtie_out +FBti0019483 661 0 F sample2.srbowtie_out +FBti0020398 0 0 F sample2.srbowtie_out FBti0020398 41 1.0 F sample2.srbowtie_out FBti0020398 59 -1.0 R sample2.srbowtie_out FBti0020398 60 -1.0 R sample2.srbowtie_out @@ -1822,6 +1955,8 @@ FBti0020398 345 1.0 F sample2.srbowtie_out FBti0020398 348 2.0 F sample2.srbowtie_out FBti0020398 446 -1.0 R sample2.srbowtie_out +FBti0020398 565 0 F sample2.srbowtie_out +FBti0019509 0 0 F sample2.srbowtie_out FBti0019509 31 2.0 F sample2.srbowtie_out FBti0019509 32 1.0 F sample2.srbowtie_out FBti0019509 34 1.0 F sample2.srbowtie_out @@ -1852,6 +1987,8 @@ FBti0019509 1133 3.0 F sample2.srbowtie_out FBti0019509 1143 3.0 F sample2.srbowtie_out FBti0019509 1152 -1.0 R sample2.srbowtie_out +FBti0019509 1209 0 F sample2.srbowtie_out +FBti0019507 0 0 F sample2.srbowtie_out FBti0019507 15 1.0 F sample2.srbowtie_out FBti0019507 114 -1.0 R sample2.srbowtie_out FBti0019507 219 -1.0 R sample2.srbowtie_out @@ -1864,6 +2001,8 @@ FBti0019507 843 -1.0 R sample2.srbowtie_out FBti0019507 926 -1.0 R sample2.srbowtie_out FBti0019507 1025 -2.0 R sample2.srbowtie_out +FBti0019507 1039 0 F sample2.srbowtie_out +FBti0019504 0 0 F sample2.srbowtie_out FBti0019504 65 4.0 F sample2.srbowtie_out FBti0019504 204 4.0 F sample2.srbowtie_out FBti0019504 232 1.0 F sample2.srbowtie_out @@ -1899,6 +2038,8 @@ FBti0019504 2985 2.0 F sample2.srbowtie_out FBti0019504 2994 -2.0 R sample2.srbowtie_out FBti0019504 3009 1.0 F sample2.srbowtie_out +FBti0019504 3082 0 F sample2.srbowtie_out +FBti0019503 0 0 F sample2.srbowtie_out FBti0019503 14 2.0 F sample2.srbowtie_out FBti0019503 98 1.0 F sample2.srbowtie_out FBti0019503 101 3.0 F sample2.srbowtie_out @@ -1916,6 +2057,8 @@ FBti0019503 293 -1.0 R sample2.srbowtie_out FBti0019503 296 1.0 F sample2.srbowtie_out FBti0019503 383 -1.0 R sample2.srbowtie_out +FBti0019503 422 0 F sample2.srbowtie_out +FBti0019502 0 0 F sample2.srbowtie_out FBti0019502 86 1.0 F sample2.srbowtie_out FBti0019502 146 1.0 F sample2.srbowtie_out FBti0019502 232 -1.0 R sample2.srbowtie_out @@ -1924,8 +2067,12 @@ FBti0019502 301 1.0 F sample2.srbowtie_out FBti0019502 695 2.0 F sample2.srbowtie_out FBti0019502 1037 1.0 F sample2.srbowtie_out +FBti0019502 1076 0 F sample2.srbowtie_out +FBti0019501 0 0 F sample2.srbowtie_out FBti0019501 494 1.0 F sample2.srbowtie_out FBti0019501 695 1.0 F sample2.srbowtie_out +FBti0019501 966 0 F sample2.srbowtie_out +FBti0019500 0 0 F sample2.srbowtie_out FBti0019500 15 1.0 F sample2.srbowtie_out FBti0019500 102 1.0 F sample2.srbowtie_out FBti0019500 247 -1.0 R sample2.srbowtie_out @@ -1934,6 +2081,8 @@ FBti0019500 515 1.0 F sample2.srbowtie_out FBti0019500 728 5.0 F sample2.srbowtie_out FBti0019500 877 1.0 F sample2.srbowtie_out +FBti0019500 1111 0 F sample2.srbowtie_out +FBti0020402 0 0 F sample2.srbowtie_out FBti0020402 44 -1.0 R sample2.srbowtie_out FBti0020402 147 1.0 F sample2.srbowtie_out FBti0020402 172 1.0 F sample2.srbowtie_out @@ -1976,6 +2125,8 @@ FBti0020402 5921 -1.0 R sample2.srbowtie_out FBti0020402 6241 1.0 F sample2.srbowtie_out FBti0020402 6329 1.0 F sample2.srbowtie_out +FBti0020402 6438 0 F sample2.srbowtie_out +FBti0020410 0 0 F sample2.srbowtie_out FBti0020410 73 -1.0 R sample2.srbowtie_out FBti0020410 126 1.0 F sample2.srbowtie_out FBti0020410 886 -1.0 R sample2.srbowtie_out @@ -2014,6 +2165,8 @@ FBti0020410 6340 -1.0 R sample2.srbowtie_out FBti0020410 6439 -1.0 R sample2.srbowtie_out FBti0020410 6739 -1.0 R sample2.srbowtie_out +FBti0020410 6752 0 F sample2.srbowtie_out +FBti0020403 0 0 F sample2.srbowtie_out FBti0020403 57 1.0 F sample2.srbowtie_out FBti0020403 99 1.0 F sample2.srbowtie_out FBti0020403 101 1.0 F sample2.srbowtie_out @@ -2023,6 +2176,8 @@ FBti0020403 869 -1.0 R sample2.srbowtie_out FBti0020403 910 -1.0 R sample2.srbowtie_out FBti0020403 1018 -1.0 R sample2.srbowtie_out +FBti0020403 1101 0 F sample2.srbowtie_out +FBti0019486 0 0 F sample2.srbowtie_out FBti0019486 299 -1.0 R sample2.srbowtie_out FBti0019486 368 -1.0 R sample2.srbowtie_out FBti0019486 384 1.0 F sample2.srbowtie_out @@ -2032,7 +2187,11 @@ FBti0019486 878 1.0 F sample2.srbowtie_out FBti0019486 1068 1.0 F sample2.srbowtie_out FBti0019486 1198 -4.0 R sample2.srbowtie_out +FBti0019486 1205 0 F sample2.srbowtie_out +FBti0019489 0 0 F sample2.srbowtie_out FBti0019489 67 -1.0 R sample2.srbowtie_out +FBti0019489 369 0 F sample2.srbowtie_out +FBti0019484 0 0 F sample2.srbowtie_out FBti0019484 15 1.0 F sample2.srbowtie_out FBti0019484 101 1.0 F sample2.srbowtie_out FBti0019484 102 1.0 F sample2.srbowtie_out @@ -2041,11 +2200,17 @@ FBti0019484 547 -2.0 R sample2.srbowtie_out FBti0019484 703 1.0 F sample2.srbowtie_out FBti0019484 961 -1.0 R sample2.srbowtie_out +FBti0019484 1084 0 F sample2.srbowtie_out +FBti0019485 0 0 F sample2.srbowtie_out FBti0019485 261 -1.0 R sample2.srbowtie_out FBti0019485 711 -2.0 R sample2.srbowtie_out FBti0019485 775 1.0 F sample2.srbowtie_out FBti0019485 881 -1.0 R sample2.srbowtie_out +FBti0019485 1075 0 F sample2.srbowtie_out +FBti0019482 0 0 F sample2.srbowtie_out FBti0019482 112 -3.0 R sample2.srbowtie_out +FBti0019482 597 0 F sample2.srbowtie_out +FBti0020400 0 0 F sample2.srbowtie_out FBti0020400 15 1.0 F sample2.srbowtie_out FBti0020400 93 -1.0 R sample2.srbowtie_out FBti0020400 127 -1.0 R sample2.srbowtie_out @@ -2360,6 +2525,15 @@ FBti0020400 8849 1.0 F sample2.srbowtie_out FBti0020400 9192 1.0 F sample2.srbowtie_out FBti0020400 9333 -1.0 R sample2.srbowtie_out +FBti0020400 9398 0 F sample2.srbowtie_out +FBti0019480 0 0 F sample2.srbowtie_out +FBti0019480 327 1.0 F sample2.srbowtie_out +FBti0019480 446 1.0 F sample2.srbowtie_out +FBti0019480 503 -3.0 R sample2.srbowtie_out +FBti0019480 594 1.0 F sample2.srbowtie_out +FBti0019480 619 1.0 F sample2.srbowtie_out +FBti0019480 669 0 F sample2.srbowtie_out +FBti0020401 0 0 F sample3.srbowtie_out FBti0020401 250 1.0 F sample3.srbowtie_out FBti0020401 274 -1.0 R sample3.srbowtie_out FBti0020401 520 -1.0 R sample3.srbowtie_out @@ -2373,13 +2547,21 @@ FBti0020401 5996 -1.0 R sample3.srbowtie_out FBti0020401 6183 -1.0 R sample3.srbowtie_out FBti0020401 6218 1.0 F sample3.srbowtie_out +FBti0020401 6348 0 F sample3.srbowtie_out +FBti0020406 0 0 F sample3.srbowtie_out FBti0020406 161 1.0 F sample3.srbowtie_out FBti0020406 697 -1.0 R sample3.srbowtie_out +FBti0020406 812 0 F sample3.srbowtie_out +FBti0019511 0 0 F sample3.srbowtie_out FBti0019511 1 0 F sample3.srbowtie_out +FBti0019511 1402 0 F sample3.srbowtie_out +FBti0019512 0 0 F sample3.srbowtie_out FBti0019512 20 1.0 F sample3.srbowtie_out FBti0019512 21 -1.0 R sample3.srbowtie_out FBti0019512 22 -1.0 R sample3.srbowtie_out FBti0019512 33 1.0 F sample3.srbowtie_out +FBti0019512 221 0 F sample3.srbowtie_out +FBti0019473 0 0 F sample3.srbowtie_out FBti0019473 191 -2.0 R sample3.srbowtie_out FBti0019473 195 -1.0 R sample3.srbowtie_out FBti0019473 198 -1.0 R sample3.srbowtie_out @@ -2429,6 +2611,8 @@ FBti0019473 4587 -1.0 R sample3.srbowtie_out FBti0019473 4860 -1.0 R sample3.srbowtie_out FBti0019473 4948 -1.0 R sample3.srbowtie_out +FBti0019473 5368 0 F sample3.srbowtie_out +FBti0019518 0 0 F sample3.srbowtie_out FBti0019518 86 1.0 F sample3.srbowtie_out FBti0019518 108 -1.0 R sample3.srbowtie_out FBti0019518 180 2.0 F sample3.srbowtie_out @@ -2440,6 +2624,8 @@ FBti0019518 709 1.0 F sample3.srbowtie_out FBti0019518 821 -1.0 R sample3.srbowtie_out FBti0019518 875 -1.0 R sample3.srbowtie_out +FBti0019518 1012 0 F sample3.srbowtie_out +FBti0019519 0 0 F sample3.srbowtie_out FBti0019519 1202 1.0 F sample3.srbowtie_out FBti0019519 1211 -1.0 R sample3.srbowtie_out FBti0019519 1325 3.0 F sample3.srbowtie_out @@ -2466,8 +2652,12 @@ FBti0019519 2037 -1.0 R sample3.srbowtie_out FBti0019519 2114 1.0 F sample3.srbowtie_out FBti0019519 2121 1.0 F sample3.srbowtie_out +FBti0019519 3897 0 F sample3.srbowtie_out +FBti0019514 0 0 F sample3.srbowtie_out FBti0019514 46 -1.0 R sample3.srbowtie_out FBti0019514 76 1.0 F sample3.srbowtie_out +FBti0019514 466 0 F sample3.srbowtie_out +FBti0019515 0 0 F sample3.srbowtie_out FBti0019515 818 1.0 F sample3.srbowtie_out FBti0019515 835 1.0 F sample3.srbowtie_out FBti0019515 905 -1.0 R sample3.srbowtie_out @@ -2484,6 +2674,8 @@ FBti0019515 2285 2.0 F sample3.srbowtie_out FBti0019515 2475 -5.0 R sample3.srbowtie_out FBti0019515 2558 -1.0 R sample3.srbowtie_out +FBti0019515 2592 0 F sample3.srbowtie_out +FBti0019516 0 0 F sample3.srbowtie_out FBti0019516 59 -1.0 R sample3.srbowtie_out FBti0019516 264 2.0 F sample3.srbowtie_out FBti0019516 500 -1.0 R sample3.srbowtie_out @@ -2492,6 +2684,8 @@ FBti0019516 737 7.0 F sample3.srbowtie_out FBti0019516 937 -2.0 R sample3.srbowtie_out FBti0019516 941 -1.0 R sample3.srbowtie_out +FBti0019516 1132 0 F sample3.srbowtie_out +FBti0019517 0 0 F sample3.srbowtie_out FBti0019517 15 1.0 F sample3.srbowtie_out FBti0019517 39 1.0 F sample3.srbowtie_out FBti0019517 59 -1.0 R sample3.srbowtie_out @@ -2520,6 +2714,8 @@ FBti0019517 581 3.0 F sample3.srbowtie_out FBti0019517 590 -8.0 R sample3.srbowtie_out FBti0019517 650 -1.0 R sample3.srbowtie_out +FBti0019517 740 0 F sample3.srbowtie_out +FBti0020404 0 0 F sample3.srbowtie_out FBti0020404 59 1.0 F sample3.srbowtie_out FBti0020404 99 1.0 F sample3.srbowtie_out FBti0020404 212 1.0 F sample3.srbowtie_out @@ -2540,6 +2736,8 @@ FBti0020404 1187 -1.0 R sample3.srbowtie_out FBti0020404 1275 -1.0 R sample3.srbowtie_out FBti0020404 1351 1.0 F sample3.srbowtie_out +FBti0020404 1470 0 F sample3.srbowtie_out +FBti0020405 0 0 F sample3.srbowtie_out FBti0020405 203 -1.0 R sample3.srbowtie_out FBti0020405 204 -1.0 R sample3.srbowtie_out FBti0020405 205 -1.0 R sample3.srbowtie_out @@ -2548,6 +2746,8 @@ FBti0020405 404 2.0 F sample3.srbowtie_out FBti0020405 413 1.0 F sample3.srbowtie_out FBti0020405 415 1.0 F sample3.srbowtie_out +FBti0020405 745 0 F sample3.srbowtie_out +FBti0019499 0 0 F sample3.srbowtie_out FBti0019499 143 1.0 F sample3.srbowtie_out FBti0019499 152 -1.0 R sample3.srbowtie_out FBti0019499 193 2.0 F sample3.srbowtie_out @@ -2594,13 +2794,19 @@ FBti0019499 1605 -1.0 R sample3.srbowtie_out FBti0019499 1606 -1.0 R sample3.srbowtie_out FBti0019499 1608 -1.0 R sample3.srbowtie_out +FBti0019499 1728 0 F sample3.srbowtie_out +FBti0019472 0 0 F sample3.srbowtie_out FBti0019472 56 1.0 F sample3.srbowtie_out FBti0019472 161 1.0 F sample3.srbowtie_out FBti0019472 264 1.0 F sample3.srbowtie_out FBti0019472 457 1.0 F sample3.srbowtie_out FBti0019472 670 1.0 F sample3.srbowtie_out FBti0019472 970 1.0 F sample3.srbowtie_out +FBti0019472 1044 0 F sample3.srbowtie_out +FBti0020396 0 0 F sample3.srbowtie_out FBti0020396 634 -1.0 R sample3.srbowtie_out +FBti0020396 1838 0 F sample3.srbowtie_out +FBti0019476 0 0 F sample3.srbowtie_out FBti0019476 154 -1.0 R sample3.srbowtie_out FBti0019476 164 -1.0 R sample3.srbowtie_out FBti0019476 337 -1.0 R sample3.srbowtie_out @@ -2614,6 +2820,8 @@ FBti0019476 1676 -3.0 R sample3.srbowtie_out FBti0019476 3052 -1.0 R sample3.srbowtie_out FBti0019476 3155 -2.0 R sample3.srbowtie_out +FBti0019476 4183 0 F sample3.srbowtie_out +FBti0019493 0 0 F sample3.srbowtie_out FBti0019493 37 1.0 F sample3.srbowtie_out FBti0019493 153 -1.0 R sample3.srbowtie_out FBti0019493 159 1.0 F sample3.srbowtie_out @@ -2869,6 +3077,8 @@ FBti0019493 4398 -3.0 R sample3.srbowtie_out FBti0019493 4409 -1.0 R sample3.srbowtie_out FBti0019493 4430 -2.0 R sample3.srbowtie_out +FBti0019493 4431 0 F sample3.srbowtie_out +FBti0019492 0 0 F sample3.srbowtie_out FBti0019492 36 1.0 F sample3.srbowtie_out FBti0019492 260 -1.0 R sample3.srbowtie_out FBti0019492 402 1.0 F sample3.srbowtie_out @@ -2877,7 +3087,11 @@ FBti0019492 529 1.0 F sample3.srbowtie_out FBti0019492 550 -1.0 R sample3.srbowtie_out FBti0019492 738 1.0 F sample3.srbowtie_out +FBti0019492 1035 0 F sample3.srbowtie_out +FBti0019495 0 0 F sample3.srbowtie_out FBti0019495 8146 -1.0 R sample3.srbowtie_out +FBti0019495 8526 0 F sample3.srbowtie_out +FBti0019494 0 0 F sample3.srbowtie_out FBti0019494 24 -1.0 R sample3.srbowtie_out FBti0019494 161 1.0 F sample3.srbowtie_out FBti0019494 210 2.0 F sample3.srbowtie_out @@ -2887,6 +3101,8 @@ FBti0019494 574 -1.0 R sample3.srbowtie_out FBti0019494 689 5.0 F sample3.srbowtie_out FBti0019494 1046 -1.0 R sample3.srbowtie_out +FBti0019494 1060 0 F sample3.srbowtie_out +FBti0020395 0 0 F sample3.srbowtie_out FBti0020395 361 1.0 F sample3.srbowtie_out FBti0020395 370 -1.0 R sample3.srbowtie_out FBti0020395 419 1.0 F sample3.srbowtie_out @@ -2907,6 +3123,8 @@ FBti0020395 846 -2.0 R sample3.srbowtie_out FBti0020395 888 1.0 F sample3.srbowtie_out FBti0020395 1052 -1.0 R sample3.srbowtie_out +FBti0020395 1082 0 F sample3.srbowtie_out +FBti0019483 0 0 F sample3.srbowtie_out FBti0019483 53 -1.0 R sample3.srbowtie_out FBti0019483 91 -1.0 R sample3.srbowtie_out FBti0019483 115 -2.0 R sample3.srbowtie_out @@ -2919,9 +3137,13 @@ FBti0019483 473 -2.0 R sample3.srbowtie_out FBti0019483 507 -1.0 R sample3.srbowtie_out FBti0019483 594 2.0 F sample3.srbowtie_out +FBti0019483 661 0 F sample3.srbowtie_out +FBti0020398 0 0 F sample3.srbowtie_out FBti0020398 114 2.0 F sample3.srbowtie_out FBti0020398 170 1.0 F sample3.srbowtie_out FBti0020398 334 6.0 F sample3.srbowtie_out +FBti0020398 565 0 F sample3.srbowtie_out +FBti0019509 0 0 F sample3.srbowtie_out FBti0019509 51 -1.0 R sample3.srbowtie_out FBti0019509 60 -1.0 R sample3.srbowtie_out FBti0019509 104 -1.0 R sample3.srbowtie_out @@ -2940,6 +3162,8 @@ FBti0019509 991 1.0 F sample3.srbowtie_out FBti0019509 1135 3.0 F sample3.srbowtie_out FBti0019509 1137 3.0 F sample3.srbowtie_out +FBti0019509 1209 0 F sample3.srbowtie_out +FBti0019507 0 0 F sample3.srbowtie_out FBti0019507 24 -1.0 R sample3.srbowtie_out FBti0019507 246 -1.0 R sample3.srbowtie_out FBti0019507 247 -5.0 R sample3.srbowtie_out @@ -2949,6 +3173,8 @@ FBti0019507 901 -2.0 R sample3.srbowtie_out FBti0019507 943 1.0 F sample3.srbowtie_out FBti0019507 958 1.0 F sample3.srbowtie_out +FBti0019507 1039 0 F sample3.srbowtie_out +FBti0019504 0 0 F sample3.srbowtie_out FBti0019504 74 -3.0 R sample3.srbowtie_out FBti0019504 94 1.0 F sample3.srbowtie_out FBti0019504 125 -2.0 R sample3.srbowtie_out @@ -2995,6 +3221,8 @@ FBti0019504 2994 -1.0 R sample3.srbowtie_out FBti0019504 2996 1.0 F sample3.srbowtie_out FBti0019504 3046 -1.0 R sample3.srbowtie_out +FBti0019504 3082 0 F sample3.srbowtie_out +FBti0019503 0 0 F sample3.srbowtie_out FBti0019503 14 1.0 F sample3.srbowtie_out FBti0019503 28 1.0 F sample3.srbowtie_out FBti0019503 100 6.0 F sample3.srbowtie_out @@ -3023,6 +3251,8 @@ FBti0019503 371 1.0 F sample3.srbowtie_out FBti0019503 374 1.0 F sample3.srbowtie_out FBti0019503 383 -1.0 R sample3.srbowtie_out +FBti0019503 422 0 F sample3.srbowtie_out +FBti0019502 0 0 F sample3.srbowtie_out FBti0019502 15 1.0 F sample3.srbowtie_out FBti0019502 43 1.0 F sample3.srbowtie_out FBti0019502 86 1.0 F sample3.srbowtie_out @@ -3035,8 +3265,12 @@ FBti0019502 870 1.0 F sample3.srbowtie_out FBti0019502 882 -2.0 R sample3.srbowtie_out FBti0019502 1062 -1.0 R sample3.srbowtie_out +FBti0019502 1076 0 F sample3.srbowtie_out +FBti0019501 0 0 F sample3.srbowtie_out FBti0019501 599 -1.0 R sample3.srbowtie_out FBti0019501 726 -1.0 R sample3.srbowtie_out +FBti0019501 966 0 F sample3.srbowtie_out +FBti0019500 0 0 F sample3.srbowtie_out FBti0019500 24 -1.0 R sample3.srbowtie_out FBti0019500 56 1.0 F sample3.srbowtie_out FBti0019500 58 1.0 F sample3.srbowtie_out @@ -3051,6 +3285,8 @@ FBti0019500 935 -1.0 R sample3.srbowtie_out FBti0019500 1034 -1.0 R sample3.srbowtie_out FBti0019500 1097 -1.0 R sample3.srbowtie_out +FBti0019500 1111 0 F sample3.srbowtie_out +FBti0020402 0 0 F sample3.srbowtie_out FBti0020402 44 -1.0 R sample3.srbowtie_out FBti0020402 301 1.0 F sample3.srbowtie_out FBti0020402 349 -1.0 R sample3.srbowtie_out @@ -3093,6 +3329,8 @@ FBti0020402 6361 1.0 F sample3.srbowtie_out FBti0020402 6367 -1.0 R sample3.srbowtie_out FBti0020402 6395 1.0 F sample3.srbowtie_out +FBti0020402 6438 0 F sample3.srbowtie_out +FBti0020410 0 0 F sample3.srbowtie_out FBti0020410 103 -1.0 R sample3.srbowtie_out FBti0020410 123 1.0 F sample3.srbowtie_out FBti0020410 197 1.0 F sample3.srbowtie_out @@ -3148,6 +3386,8 @@ FBti0020410 6479 -1.0 R sample3.srbowtie_out FBti0020410 6629 -1.0 R sample3.srbowtie_out FBti0020410 6647 1.0 F sample3.srbowtie_out +FBti0020410 6752 0 F sample3.srbowtie_out +FBti0020403 0 0 F sample3.srbowtie_out FBti0020403 40 1.0 F sample3.srbowtie_out FBti0020403 60 1.0 F sample3.srbowtie_out FBti0020403 161 2.0 F sample3.srbowtie_out @@ -3158,6 +3398,8 @@ FBti0020403 869 -1.0 R sample3.srbowtie_out FBti0020403 908 -1.0 R sample3.srbowtie_out FBti0020403 1014 -1.0 R sample3.srbowtie_out +FBti0020403 1101 0 F sample3.srbowtie_out +FBti0019486 0 0 F sample3.srbowtie_out FBti0019486 299 -1.0 R sample3.srbowtie_out FBti0019486 468 -1.0 R sample3.srbowtie_out FBti0019486 529 -1.0 R sample3.srbowtie_out @@ -3166,7 +3408,11 @@ FBti0019486 715 1.0 F sample3.srbowtie_out FBti0019486 784 -1.0 R sample3.srbowtie_out FBti0019486 1008 -1.0 R sample3.srbowtie_out +FBti0019486 1205 0 F sample3.srbowtie_out +FBti0019489 0 0 F sample3.srbowtie_out FBti0019489 1 0 F sample3.srbowtie_out +FBti0019489 369 0 F sample3.srbowtie_out +FBti0019484 0 0 F sample3.srbowtie_out FBti0019484 101 1.0 F sample3.srbowtie_out FBti0019484 138 -1.0 R sample3.srbowtie_out FBti0019484 247 -1.0 R sample3.srbowtie_out @@ -3176,11 +3422,17 @@ FBti0019484 703 5.0 F sample3.srbowtie_out FBti0019484 903 -2.0 R sample3.srbowtie_out FBti0019484 952 2.0 F sample3.srbowtie_out +FBti0019484 1084 0 F sample3.srbowtie_out +FBti0019485 0 0 F sample3.srbowtie_out FBti0019485 220 1.0 F sample3.srbowtie_out FBti0019485 711 -1.0 R sample3.srbowtie_out FBti0019485 796 -1.0 R sample3.srbowtie_out +FBti0019485 1075 0 F sample3.srbowtie_out +FBti0019482 0 0 F sample3.srbowtie_out FBti0019482 112 -1.0 R sample3.srbowtie_out FBti0019482 340 -1.0 R sample3.srbowtie_out +FBti0019482 597 0 F sample3.srbowtie_out +FBti0020400 0 0 F sample3.srbowtie_out FBti0020400 15 2.0 F sample3.srbowtie_out FBti0020400 40 1.0 F sample3.srbowtie_out FBti0020400 84 1.0 F sample3.srbowtie_out @@ -3430,3 +3682,14 @@ FBti0020400 9275 1.0 F sample3.srbowtie_out FBti0020400 9306 -1.0 R sample3.srbowtie_out FBti0020400 9334 -1.0 R sample3.srbowtie_out +FBti0020400 9398 0 F sample3.srbowtie_out +FBti0019480 0 0 F sample3.srbowtie_out +FBti0019480 23 1.0 F sample3.srbowtie_out +FBti0019480 384 1.0 F sample3.srbowtie_out +FBti0019480 493 5.0 F sample3.srbowtie_out +FBti0019480 501 -1.0 R sample3.srbowtie_out +FBti0019480 502 -7.0 R sample3.srbowtie_out +FBti0019480 503 -1.0 R sample3.srbowtie_out +FBti0019480 594 1.0 F sample3.srbowtie_out +FBti0019480 619 1.0 F sample3.srbowtie_out +FBti0019480 669 0 F sample3.srbowtie_out
--- a/test-data/Size_distribution_dataframe.tab Sun Sep 18 12:55:27 2016 -0400 +++ b/test-data/Size_distribution_dataframe.tab Mon Sep 19 06:16:21 2016 -0400 @@ -879,6 +879,28 @@ FBti0020400 28 16.0 F sample1.srbowtie_out FBti0020400 29 0.0 F sample1.srbowtie_out FBti0020400 30 0 F sample1.srbowtie_out +FBti0019480 20 0 R sample1.srbowtie_out +FBti0019480 21 0 R sample1.srbowtie_out +FBti0019480 22 -1.0 R sample1.srbowtie_out +FBti0019480 23 0 R sample1.srbowtie_out +FBti0019480 24 -2.0 R sample1.srbowtie_out +FBti0019480 25 -1.0 R sample1.srbowtie_out +FBti0019480 26 0.0 R sample1.srbowtie_out +FBti0019480 27 0 R sample1.srbowtie_out +FBti0019480 28 0 R sample1.srbowtie_out +FBti0019480 29 0 R sample1.srbowtie_out +FBti0019480 30 0 R sample1.srbowtie_out +FBti0019480 20 0 F sample1.srbowtie_out +FBti0019480 21 0 F sample1.srbowtie_out +FBti0019480 22 0.0 F sample1.srbowtie_out +FBti0019480 23 0 F sample1.srbowtie_out +FBti0019480 24 0.0 F sample1.srbowtie_out +FBti0019480 25 1.0 F sample1.srbowtie_out +FBti0019480 26 2.0 F sample1.srbowtie_out +FBti0019480 27 0 F sample1.srbowtie_out +FBti0019480 28 0 F sample1.srbowtie_out +FBti0019480 29 0 F sample1.srbowtie_out +FBti0019480 30 0 F sample1.srbowtie_out FBti0020401 20 -2.0 R sample2.srbowtie_out FBti0020401 21 0 R sample2.srbowtie_out FBti0020401 22 0.0 R sample2.srbowtie_out @@ -1759,6 +1781,28 @@ FBti0020400 28 15.0 F sample2.srbowtie_out FBti0020400 29 1.0 F sample2.srbowtie_out FBti0020400 30 0 F sample2.srbowtie_out +FBti0019480 20 0.0 R sample2.srbowtie_out +FBti0019480 21 0 R sample2.srbowtie_out +FBti0019480 22 0 R sample2.srbowtie_out +FBti0019480 23 0 R sample2.srbowtie_out +FBti0019480 24 -2.0 R sample2.srbowtie_out +FBti0019480 25 -1.0 R sample2.srbowtie_out +FBti0019480 26 0.0 R sample2.srbowtie_out +FBti0019480 27 0.0 R sample2.srbowtie_out +FBti0019480 28 0 R sample2.srbowtie_out +FBti0019480 29 0 R sample2.srbowtie_out +FBti0019480 30 0 R sample2.srbowtie_out +FBti0019480 20 1.0 F sample2.srbowtie_out +FBti0019480 21 0 F sample2.srbowtie_out +FBti0019480 22 0 F sample2.srbowtie_out +FBti0019480 23 0 F sample2.srbowtie_out +FBti0019480 24 1.0 F sample2.srbowtie_out +FBti0019480 25 0.0 F sample2.srbowtie_out +FBti0019480 26 1.0 F sample2.srbowtie_out +FBti0019480 27 1.0 F sample2.srbowtie_out +FBti0019480 28 0 F sample2.srbowtie_out +FBti0019480 29 0 F sample2.srbowtie_out +FBti0019480 30 0 F sample2.srbowtie_out FBti0020401 20 -1.0 R sample3.srbowtie_out FBti0020401 21 0.0 R sample3.srbowtie_out FBti0020401 22 -1.0 R sample3.srbowtie_out @@ -2639,3 +2683,25 @@ FBti0020400 28 12.0 F sample3.srbowtie_out FBti0020400 29 0 F sample3.srbowtie_out FBti0020400 30 0 F sample3.srbowtie_out +FBti0019480 20 0 R sample3.srbowtie_out +FBti0019480 21 -1.0 R sample3.srbowtie_out +FBti0019480 22 0.0 R sample3.srbowtie_out +FBti0019480 23 -2.0 R sample3.srbowtie_out +FBti0019480 24 -5.0 R sample3.srbowtie_out +FBti0019480 25 -1.0 R sample3.srbowtie_out +FBti0019480 26 0.0 R sample3.srbowtie_out +FBti0019480 27 0.0 R sample3.srbowtie_out +FBti0019480 28 0 R sample3.srbowtie_out +FBti0019480 29 0 R sample3.srbowtie_out +FBti0019480 30 0 R sample3.srbowtie_out +FBti0019480 20 0 F sample3.srbowtie_out +FBti0019480 21 0.0 F sample3.srbowtie_out +FBti0019480 22 1.0 F sample3.srbowtie_out +FBti0019480 23 0.0 F sample3.srbowtie_out +FBti0019480 24 3.0 F sample3.srbowtie_out +FBti0019480 25 2.0 F sample3.srbowtie_out +FBti0019480 26 2.0 F sample3.srbowtie_out +FBti0019480 27 1.0 F sample3.srbowtie_out +FBti0019480 28 0 F sample3.srbowtie_out +FBti0019480 29 0 F sample3.srbowtie_out +FBti0019480 30 0 F sample3.srbowtie_out
--- a/tool_dependencies.xml Sun Sep 18 12:55:27 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bowtie" version="0.12.7"> - <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="pysam" version="0.7.7"> - <repository changeset_revision="0a5141bdf9d0" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="numpy" version="1.9"> - <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="R" version="3.1.2"> - <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="biocbasics" version="2.14"> - <repository changeset_revision="f0ef1a7b157e" name="package_biocbasics_2_14" owner="mvdbeek" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>