diff STACKS_sort_read_pairs.py @ 0:d6ba40f6c824

first commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/STACKS_sort_read_pairs.py	Mon Aug 24 09:29:12 2015 +0000
@@ -0,0 +1,109 @@
+#!/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 stacks import *
+
+"""
+
+Created by Yvan Le Bras
[e-mail]
+
+Last modifications : 02/17/2014
+
+WARNING :
+
+STACKS_sort_read_pairs.py needs:
+
+- STACKS scripts in your $PATH
+
+These scripts are available after compiling the sources of STACKS :
+
+http://creskolab.uoregon.edu/stacks/
+
+or with the galaxy_stacks package in the Genouest toolshed
+
+
+"""
+
+def __main__():
+	
+
+	# create the working dir
+	os.mkdir("sort_read_outputs")
+	os.mkdir("assembly_outputs")
+	os.mkdir("samples_inputs")
+        os.mkdir("stacks_inputs")
+
+	# arguments recuperation
+	parser = optparse.OptionParser()
+	parser.add_option("-a")
+	parser.add_option("-e")
+	parser.add_option("-b")
+	parser.add_option("-c")
+   	parser.add_option("-d")
+   	parser.add_option("-o")
+	(options, args) = parser.parse_args()
+
+	# edit the command line
+	cmd_line1 = ["sort_read_pairs.pl"]
+
+	#parse config files and create symlink if individual files are selected
+
+	# STACKS_archive
+	# check if zipped files are into the tab
+	extract_compress_files(options.a, os.getcwd()+"/stacks_inputs")
+
+	# samples_archive
+	# check if zipped files are into the tab and change tab content
+	extract_compress_files(options.e, os.getcwd()+"/samples_inputs")
+		
+	# create the sort_read_pairs command input line
+	cmd_line1.extend(["-p", "stacks_inputs", "-s", "samples_inputs", "-o", "sort_read_outputs"])
+
+	if options.b:
+		cmd_line1.extend(["-w", options.b])
+	if options.c:
+		cmd_line1.extend(["-r", options.c])
+
+	# exec command line 1 
+	p1 = subprocess.Popen(cmd_line1)
+        p1.communicate()
+
+	# parse all files list and remove empty files from the output dir
+        for fasta_file in glob.glob("sort_read_outputs/*"):
+                if os.stat(fasta_file).st_size==0:
+                        print "File "+fasta_file+" is empty"
+                        os.remove(fasta_file)
+        
+
+	# create the exec_velvet command input line
+	cmd_line2 = ["exec_velvet.pl"]
+	cmd_line2.extend(["-s", "sort_read_outputs", "-o", "assembly_outputs"])
+        cmd_line2.append("-c")
+
+	if options.d:
+		cmd_line2.extend(["-M", options.d])
+
+	# version
+	#cmd = 'sort_read_pairs.pl'+cmd_files+" "+cmd_options+" 2>&1"
+	#cmd2 = 'exec_velvet.pl'+cmd_files2+" -c -e /softs/local/velvet/velvet_1.2.03/ "+cmd_options2+" 2>&1"
+	
+	# launch the command line 2 
+        p2 = subprocess.Popen(cmd_line2)
+        p2.communicate()
+
+	# get collated.fa file
+        try:
+	    shutil.copy("assembly_outputs/collated.fa", options.o)
+	except:
+            print "No result file"
+            sys.exit(1)
+
+if __name__ == "__main__": __main__()