diff STACKS_clone_filter.py @ 0:42e64fbf4609 draft

planemo upload commit 60a090d1dc89c2eb383feeb35cd6078b9130e0e5-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/STACKS_clone_filter.py	Tue Feb 02 21:15:50 2016 -0500
@@ -0,0 +1,48 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+import shutil
+import subprocess
+import argparse
+
+
+def __main__():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-f', type=str)
+    parser.add_argument('-fwd', type=str)
+    parser.add_argument('-rev', type=str)
+
+    #parser.add_argument('-k', action='store_true')
+
+    options = parser.parse_args()
+
+    # create the working dir
+    os.mkdir('job_outputs')
+    os.chdir('job_outputs')
+
+    # STACKS_archive
+    # check if zipped files are into the tab
+    extract_compress_files(options.P, os.getcwd())
+
+    # create the populations command input line
+    cmd_line=['clone_filter']
+    if options.f is not None:
+        cmd_line.extend(['-f', options.f])
+    else:
+        cmd_line.extend(['-1', options.fwd])
+        cmd_line.extend(['-2', options.rev])
+
+    print "[CMD]:"+' '.join(cmd_line)
+    subprocess.call(cmd_line)
+
+    # postprocesses
+    clean_files = glob.glob('*.fq')
+    if options.f is not None:
+        shutil.copy(clean_files[0], 'clean.fq')
+    else:
+        shutil.copy(clean_files[0], 'fwd.fq')
+        shutil.copy(clean_files[1], 'rev.fq')
+
+
+if __name__ == '__main__':
+    __main__()