diff structure-923cc9e6aa30/Structureharvester.py @ 0:2c0b270dae70 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/structure-923cc9e6aa30/Structureharvester.py	Thu Sep 14 08:33:05 2017 -0400
@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+
+import sys, re
+import os
+import tempfile
+import shutil, subprocess, glob
+import optparse
+from os.path import basename
+import zipfile, tarfile, gzip
+from galaxy.datatypes.checkers import *
+from adlib import *
+
+"""
+
+Created by Yvan Le Bras
[e-mail]
+
+Last modifications : 01/10/2014
+
+"""
+
+
+def __main__():
+	
+
+	# arguments recuperation
+	parser = optparse.OptionParser()
+	parser.add_option("-P")
+	parser.add_option("--evanno")
+	parser.add_option("--clumpp")
+	# multifile management
+	parser.add_option("--logfile")
+	# output management
+        parser.add_option("--id")
+        parser.add_option("--workdir")
+        parser.add_option("--compress_output")
+        # additionnal outputs
+        parser.add_option("--total_output")
+	(options, args) = parser.parse_args()
+
+        # create the working dir
+        tmp_dir = tempfile.mkdtemp(dir=options.workdir)
+        tmp_output_dir = tempfile.mkdtemp(dir=tmp_dir)
+
+	print tmp_dir 
+
+	# Structure_archive
+	
+	# parse config files
+	tab_files=galaxy_config_to_tabfiles_for_STACKS(options.P)
+
+	# check if zipped files are into the tab
+	extract_compress_files_from_tabfiles(tab_files, tmp_dir)
+
+	# create the structure harvester command input line
+	cmd_files=" --dir "+tmp_dir+" --out "+tmp_output_dir+" "
+		
+	# create the populations command line
+	cmd_options=""
+
+	if options.evanno and options.evanno == 'true':
+		cmd_options+=" --evanno "
+	if options.clumpp and options.clumpp == 'true':
+		cmd_options+=" --clumpp "
+
+
+	#print " "+cmd_files+" "+cmd_options
+
+	# launch the command line
+	
+	#dev command
+	cmd = '/local/galaxy/structureharv/structureHarvester.py'+cmd_files+" "+cmd_options+" 2>&1"
+
+	#command with dependencies installed
+	#cmd = 'structureHarvester.py'+cmd_files+" "+cmd_options+" 2>&1"
+	proc = subprocess.Popen( args=cmd, shell=True )
+	returncode = proc.wait()
+
+	# postprocesses
+        if os.path.exists(tmp_output_dir+'/summary.txt'):
+                os.system('mv '+tmp_output_dir+'/summary.txt '+options.logfile)
+        else:
+                sys.stderr.write('Error in StructureHarvester execution; Please read the additional output (stdout)\n')
+
+
+	print "\n[INFO] : "+cmd
+
+        # copy all files inside tmp_dir into workdir or into an archive	
+        list_files = glob.glob(tmp_output_dir+'/*')
+
+	# if compress output is total
+	if options.compress_output == 'total':
+		mytotalzipfile=zipfile.ZipFile(tmp_output_dir+'/total.zip.temp', 'w')
+
+		os.chdir(tmp_output_dir)
+		for i in list_files:
+			mytotalzipfile.write(os.path.basename(i))
+
+		# return the unique archive
+		os.system("mv "+tmp_output_dir+'/total.zip.temp'+" "+options.total_output)
+
+	# if compress output is default
+	else:
+		for i in list_files:
+			command = "mv "+i+" "+options.workdir+ "/primary_" + options.id + "_" + os.path.basename(i).replace("_", ".") + "_visible_tabular"
+			proc = subprocess.Popen( args=command, shell=True )
+			returncode = proc.wait()	
+
+	
+	#clean up temp files
+	shutil.rmtree( tmp_dir )
+
+
+
+if __name__ == "__main__": __main__()
+
+
+
+
+