diff STACKS_prepare_population_map.py @ 0:d6ba40f6c824

first commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/STACKS_prepare_population_map.py	Mon Aug 24 09:29:12 2015 +0000
@@ -0,0 +1,74 @@
+#!/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 Cyril Monjeaud
[e-mail]
+
+Last modifications : 01/10/2014
+
+WARNING :
+
+STACKS_denovomap.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 (http://toolshed.genouest.org)
+
+"""
+def __main__():
+	
+	# arguments recuperation
+	parser = optparse.OptionParser()
+	parser.add_option("-f")
+	parser.add_option("-s")
+	parser.add_option("-t")
+	parser.add_option("-o")
+	parser.add_option("-d")
+	(options, args) = parser.parse_args()
+
+	# create the working dir
+	tmp_dir = tempfile.mkdtemp(dir=options.d)
+
+	print tmp_dir
+	#os.chdir(tmp_dir)
+
+	# parse config files
+	tab_fq_files=galaxy_config_to_tabfiles_for_STACKS(options.f)
+
+	# check if zipped files are into the tab and change tab content
+	extract_compress_files_from_tabfiles(tab_fq_files, tmp_dir)
+
+	# generate population map for denovo map
+	if not options.s:
+		generate_popmap_for_denovo(tab_fq_files, options.t, options.o)
+	else:
+		# parse config files
+		tab_sam_files=galaxy_config_to_tabfiles_for_STACKS(options.s)
+		extract_compress_files_from_tabfiles(tab_sam_files, tmp_dir)
+		generate_popmap_for_refmap(tab_fq_files, tab_sam_files, options.t, options.o)
+	
+
+	#clean up temp files
+	shutil.rmtree( tmp_dir )
+
+	
+	
+
+
+
+if __name__ == "__main__": __main__()