# HG changeset patch # User cmonjeau # Date 1441892301 0 # Node ID d085f995d556999b9fead81196cd2bf7b1c42e21 # Parent 1478d48df8c7287dcb72b7853feb760552b1ec2b remove prepare_commet and change/add packages diff -r 1478d48df8c7 -r d085f995d556 commet.py --- a/commet.py Thu Sep 10 09:59:53 2015 +0000 +++ b/commet.py Thu Sep 10 13:38:21 2015 +0000 @@ -1,6 +1,6 @@ #!/usr/bin/env python import sys, tempfile, subprocess, glob -import os, re, shutil, optparse +import os, re, shutil, argparse import zipfile, tarfile, gzip from os.path import basename @@ -13,7 +13,7 @@ http://github.com/pierrepeterlongo/commet -or with the galaxy_commet package in the GenOuest toolshed (coming soon) +or with the package_commet package in the GenOuest toolshed and the main toolshed NOTE : @@ -25,69 +25,51 @@ def __main__(): # arguments recuperation - parser = optparse.OptionParser() - parser.add_option("--input", dest="input") - parser.add_option("-k", dest="kmer") - parser.add_option("-t", dest="minsharedkmer") - parser.add_option("-l", dest="minlengthread") - parser.add_option("-n", dest="maxn") - parser.add_option("-e", dest="minshannonindex") - parser.add_option("-m", dest="maxreads") + parser = argparse.ArgumentParser() + + parser.add_argument("--set", dest="set", action='append') + parser.add_argument("-k", dest="kmer") + parser.add_argument("-t", dest="minsharedkmer") + parser.add_argument("-l", dest="minlengthread") + parser.add_argument("-n", dest="maxn") + parser.add_argument("-e", dest="minshannonindex") + parser.add_argument("-m", dest="maxreads") - parser.add_option("--output") - parser.add_option("--output_vectors") - parser.add_option("--output_dendro") - parser.add_option("--output_logs") - parser.add_option("--output_matrix") - parser.add_option("--output_heatmap1") - parser.add_option("--output_heatmap2") - parser.add_option("--output_heatmap3") + parser.add_argument("--output") + parser.add_argument("--output_vectors") + parser.add_argument("--output_dendro") + parser.add_argument("--output_matrix") + parser.add_argument("--output_heatmap1") + parser.add_argument("--output_heatmap2") + parser.add_argument("--output_heatmap3") - (options, args) = parser.parse_args() - + options = parser.parse_args() # copy R script into the current dir shutil.copy(os.environ['RSCRIPTS']+"/heatmap.r", os.getcwd()) shutil.copy(os.environ['RSCRIPTS']+"/dendro.R", os.getcwd()) - # remove the first line of the input file - commet_file = open(options.input, "r") - commet_file_clean = open("commet_clean_file", "w") - - # delete the first line - commet_file.readline() - for line in commet_file: - commet_file_clean.write(line) - - # close files - commet_file.close() - commet_file_clean.close() + # prepare input file + commet_file=open('commet_config_file', 'w') + + for set in options.set: + clean_set=set.replace(',', ';').replace('::', ':') + commet_file.write(clean_set+"\n") + commet_file.close() # edit the command line cmd_line=[] cmd_line.append("Commet.py") - cmd_line.extend(["commet_clean_file","-b",os.environ['BINARIES'],"-k",options.kmer,"-t",options.minsharedkmer,"-l",options.minlengthread,"-e",options.minshannonindex]) + cmd_line.extend(["commet_config_file","-b",os.environ['BINARIES'],"-k",options.kmer,"-t",options.minsharedkmer,"-l",options.minlengthread,"-e",options.minshannonindex]) # add options if options.maxn: - - #cmd_line += ' -n '+options.maxn+' -m '+options.maxreads+' > '+options.output+' 2>>'+options.output cmd_line.extend(["-n",options.maxn,"-m",options.maxreads]) - #else: - #cmd_line += ' > '+options.output+' 2>>'+options.output # execute job - p=subprocess.Popen(cmd_line, - stdout=subprocess.PIPE,stderr=subprocess.PIPE) - - stdoutput, stderror = p.communicate() + p=subprocess.call(cmd_line) - # log file - logfile=open(options.output, "w") - logfile.write("[COMMAND LINE]"+' '.join(cmd_line)+"\n\n") - logfile.write(str(stdoutput)) - logfile.write(str(stderror)) - logfile.close() + print "[COMMAND LINE]"+' '.join(cmd_line) # copy .bv files inside a .bv archive tmp_output_dir=os.getcwd()+"/output_commet/" @@ -120,10 +102,13 @@ shutil.move(tmp_output_dir+'matrix.zip.temp', options.output_matrix) # outputs - shutil.move(tmp_output_dir+'dendrogram_normalized.png', options.output_dendro) - shutil.move(tmp_output_dir+'heatmap_normalized.png', options.output_heatmap1) - shutil.move(tmp_output_dir+'heatmap_percentage.png', options.output_heatmap2) - shutil.move(tmp_output_dir+'heatmap_plain.png', options.output_heatmap3) + try: + shutil.move(tmp_output_dir+'dendrogram_normalized.png', options.output_dendro) + shutil.move(tmp_output_dir+'heatmap_percentage.png', options.output_heatmap2) + shutil.move(tmp_output_dir+'heatmap_normalized.png', options.output_heatmap1) + shutil.move(tmp_output_dir+'heatmap_plain.png', options.output_heatmap3) + except: + print "There is a problem with gplots execution" if __name__ == "__main__": __main__() diff -r 1478d48df8c7 -r d085f995d556 commet.xml --- a/commet.xml Thu Sep 10 09:59:53 2015 +0000 +++ b/commet.xml Thu Sep 10 13:38:21 2015 +0000 @@ -2,12 +2,13 @@ COmpare Multiple METagenomes commet - R - ggplot2 + R commet.py ---input $input +#for $set in $sets + --set ${set.setname}::${set.reads} +#end for -k $kmer -t $minsharedkmer -l $minlengthread @@ -19,7 +20,6 @@ --output $output --output_vectors $output_vectors --output_dendro $output_dendro ---output_logs $output_logs --output_matrix $output_matrix --output_heatmap1 $output_heatmap1 --output_heatmap2 $output_heatmap2 @@ -28,7 +28,10 @@ - + + + + @@ -44,9 +47,7 @@ - - @@ -55,6 +56,9 @@ + + + **Description** diff -r 1478d48df8c7 -r d085f995d556 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Thu Sep 10 13:38:21 2015 +0000 @@ -0,0 +1,4 @@ + + + + diff -r 1478d48df8c7 -r d085f995d556 tool_dependencies.xml --- a/tool_dependencies.xml Thu Sep 10 09:59:53 2015 +0000 +++ b/tool_dependencies.xml Thu Sep 10 13:38:21 2015 +0000 @@ -3,11 +3,7 @@ - - + + - - - -