diff filter-below-abund.py @ 0:d5a18dd63529 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter-below-abund.py	Wed Nov 11 09:47:38 2015 -0500
@@ -0,0 +1,87 @@
+#! /usr/bin/env python
+# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# Copyright (C) 2011-2015, Michigan State University.
+# Copyright (C) 2015, The Regents of the University of California.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+#     * Redistributions of source code must retain the above copyright
+#       notice, this list of conditions and the following disclaimer.
+#
+#     * Redistributions in binary form must reproduce the above
+#       copyright notice, this list of conditions and the following
+#       disclaimer in the documentation and/or other materials provided
+#       with the distribution.
+#
+#     * Neither the name of the Michigan State University nor the names
+#       of its contributors may be used to endorse or promote products
+#       derived from this software without specific prior written
+#       permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contact: [e-mail]
+from __future__ import print_function
+import sys
+import os
+import khmer
+from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter
+
+WORKER_THREADS = 8
+GROUPSIZE = 100
+
+CUTOFF = 50
+
+###
+
+
+def main():
+    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('making hashtable')
+    ht = khmer.load_countgraph(counting_ht)
+    K = ht.ksize()
+
+    for infile in infiles:
+        print('filtering', infile)
+        outfile = os.path.basename(infile) + '.below'
+
+        outfp = open(outfile, 'w')
+
+        def process_fn(record, ht=ht):
+            name = record['name']
+            seq = record['sequence']
+            if 'N' in seq:
+                return None, None
+
+            trim_seq, trim_at = ht.trim_below_abundance(seq, CUTOFF)
+
+            if trim_at >= K:
+                return name, trim_seq
+
+            return None, None
+
+        tsp = ThreadedSequenceProcessor(process_fn, WORKER_THREADS, GROUPSIZE)
+
+        tsp.start(verbose_fasta_iter(infile), outfp)
+
+if __name__ == '__main__':
+    main()