Galaxy - cummeRbund Output

# HG changeset patch # User cjav # Date 1329332858 18000 # Node ID 8e13da66d9b8e8a434ddc4a3f413711186a4c074 # Parent a919368ed298421e66c073ec2192e44f02c08d7d Deleted selected files diff -r a919368ed298 -r 8e13da66d9b8 cummerbund_wrapper.py --- a/cummerbund_wrapper.py Wed Feb 15 14:02:42 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ -#!/usr/bin/env python - -### Runs "r_script" and generates a HTML report -### Inspired on cuffdiff_wrapper.py and gatk_wrapper.py -### Carlos Borroto - -import optparse, os, shutil, subprocess, sys, tempfile - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - -def html_report_from_directory( html_out, dir ): - html_out.write( '\n\nGalaxy - cummeRbund Output\n\n\n

\n\n\n' ) - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - - # wrapper options - parser.add_option('', '--r-script', dest='r_script', help='R script') - parser.add_option('', '--html-report-from-directory', dest='html_report_from_directory', type="string", nargs=2, help='"Target HTML File" "Directory"') - - (options, args) = parser.parse_args() - - (html_filename, html_dir) = options.html_report_from_directory - - # Make html report directory for output. - os.mkdir( html_dir ) - - # Make a tmp dir - tmp_dir = tempfile.mkdtemp( prefix='tmp-cummeRbund-' ) - - # Build command. - cmd = ( "Rscript --vanilla %s" % options.r_script ) - - # Debugging. - print cmd - - # Run command. - try: - tmp_name = tempfile.NamedTemporaryFile( dir=tmp_dir ).name - tmp_stderr = open( tmp_name, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=html_dir, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - - # Get stderr, allowing for case where it's very large. - tmp_stderr = open( tmp_name, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - - # Error checking. - if returncode != 0: - raise Exception, stderr - except Exception, e: - stop_err( 'Error running R script. ' + str( e ) ) - - # write the html report - html_report_from_directory( open( html_filename, 'wb' ), html_dir ) - - # Clean up temp dirs - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - -if __name__=="__main__": __main__() diff -r a919368ed298 -r 8e13da66d9b8 cummerbund_wrapper.xml --- a/cummerbund_wrapper.xml Wed Feb 15 14:02:42 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,302 +0,0 @@ - - - R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output - - - cummerbund_wrapper.py - --r-script ${script_file} - --html-report-from-directory "${output_html}" "${output_html.files_path}" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - backend_database_source['backend_database_selector'] == "cuffdiff_output" - - - - - - R - - - - - - - - - ---> - - - -## Feature Selection ## -get_features <- function(myGenes, f="gene") { - if (f == "isoforms") - return(isoforms(myGenes)) - else if (f == "tss") - return(TSS(myGenes)) - else if (f == "cds") - return(CDS(myGenes)) - else - return(myGenes) -} - -## Main Function ## - -## Load cummeRbund library -library("cummeRbund") - -## Initialize cuff object -cuff <- readCufflinks(dir = "", -#if $backend_database_source.backend_database_selector == "cuffdiff_output": - dbFile = "${output_database}", - geneFPKM = "${genes_fpkm_tracking}", - geneDiff = "${genes_exp}", - isoformFPKM = "${isoforms_fpkm_tracking}", - isoformDiff = "${isoforms_exp}", - TSSFPKM = "${tss_groups_fpkm_tracking}", - TSSDiff = "${tss_groups_exp}", - CDSFPKM = "${cds_fpkm_tracking}", - CDSExpDiff = "${cds_exp_diff}", - CDSDiff = "${cds_diff}", - promoterFile = "${promoters_diff}", - splicingFile = "${splicing_diff}", - rebuild = T) -#else: - dbFile = "${backend_database_source.input_database}", - rebuild = F) -#end if - -#for $i, $p in enumerate($plots, start=1): - #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type']) -png(filename = "${filename}", width = ${p.width}, height = ${p.height}) - - ## Density plot ## - #if $p.plot['type'] == "density": -csDensity(genes(cuff)) -devname = dev.off() - - ## Boxplot ## - #elif $p.plot['type'] == "boxplot": -csBoxplot(genes(cuff)) -devname = dev.off() - - ## Scatter ## - #elif $p.plot['type'] == "scatter": - #if $p.plot.multiple_genes['multiple_genes_selector']: -myGeneIds <- c() - #for $g in $p.plot.multiple_genes['genes']: -myGeneIds <- c(myGeneIds, "$g['gene_id']") - #end for -myGenes <- getGenes(cuff, myGeneIds) -csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) - #else -csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) - #end if -devname = dev.off() - - ## Volcano ## - #elif $p.plot['type'] == "volcano": - #if $p.plot.multiple_genes['multiple_genes_selector']: -myGeneIds <- c() - #for $g in $p.plot.multiple_genes['genes']: -myGeneIds <- c(myGeneIds, "$g['gene_id']") - #end for -myGenes <- getGenes(cuff, myGeneIds) -csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}") - #else -csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}") - #end if -devname = dev.off() - - ## Heatmap ## - #elif $p.plot['type'] == "heatmap": -myGeneIds <- c() - #for $g in $p.plot.genes: -myGeneIds <- c(myGeneIds, "$g['gene_id']") - #end for -myGenes <- getGenes(cuff, myGeneIds) -csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}") -devname = dev.off() - - ## Cluster ## - #elif $p.plot['type'] == "cluster": -myGeneIds <- c() - #for $g in $p.plot.genes: -myGeneIds <- c(myGeneIds, "$g['gene_id']") - #end for -myGenes <- getGenes(cuff, myGeneIds) -csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}") -devname = dev.off() - - ## Expression Plot ## - #elif $p.plot['type'] == "expressionplot": -myGeneId <- "$p.plot.gene_id" -myGenes <- getGenes(cuff, myGeneId) -expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}") -devname = dev.off() - - ## Expression Bar Plot ## - #elif $p.plot['type'] == "expressionbarplot": -myGeneId <- "$p.plot.gene_id" -myGenes <- getGenes(cuff, myGeneId) -expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}") -devname = dev.off() - #end if - -#end for - - - - -This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. - - - diff -r a919368ed298 -r 8e13da66d9b8 datatypes_conf.xml --- a/datatypes_conf.xml Wed Feb 15 14:02:42 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - -