diff filter-below-abund.py @ 60:fe697e0cb24a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty

--- a/filter-below-abund.py	Mon Aug 18 07:02:05 2014 -0400
+++ b/filter-below-abund.py	Tue Jul 07 11:59:39 2015 -0400
@@ -1,12 +1,12 @@
-#! /usr/bin/env python2
+#! /usr/bin/env python
 #
-# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2013. It is licensed under
-# the three-clause BSD license; see doc/LICENSE.txt.
+# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# the three-clause BSD license; see LICENSE.
 # Contact: [e-mail]
 #
+from __future__ import print_function
 import sys
-import screed.fasta
 import os
 import khmer
 from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter
@@ -23,17 +23,17 @@
     counting_ht = sys.argv[1]
     infiles = sys.argv[2:]
 
-    print 'file with ht: %s' % counting_ht
-    print '-- settings:'
-    print 'N THREADS', WORKER_THREADS
-    print '--'
+    print('file with ht: %s' % counting_ht)
+    print('-- settings:')
+    print('N THREADS', WORKER_THREADS)
+    print('--')
 
-    print 'making hashtable'
+    print('making hashtable')
     ht = khmer.load_counting_hash(counting_ht)
     K = ht.ksize()
 
     for infile in infiles:
-        print 'filtering', infile
+        print('filtering', infile)
         outfile = os.path.basename(infile) + '.below'
 
         outfp = open(outfile, 'w')