diff STACKS_clone_filter.py @ 5:1a5ebb16aaea draft

planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty

--- a/STACKS_clone_filter.py	Wed Feb 03 10:58:13 2016 -0500
+++ b/STACKS_clone_filter.py	Thu Feb 04 07:50:26 2016 -0500
@@ -1,9 +1,11 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 
-import shutil
+import argparse
+import glob
+import os
 import subprocess
-import argparse
+import shutil
 
 
 def __main__():
@@ -20,10 +22,6 @@
     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:
@@ -36,7 +34,7 @@
     subprocess.call(cmd_line)
 
     # postprocesses
-    clean_files = glob.glob('*.fq')
+    clean_files = glob.glob('*.fq*')
     if options.f is not None:
         shutil.copy(clean_files[0], 'clean.fq')
     else: