comparison 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

59:08a599cf71d0

#! /usr/bin/env python2
#
# 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.
# Contact: [e-mail]
#
import sys
import screed.fasta
import os
import khmer
from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter

WORKER_THREADS = 8

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_counting_hash(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):

60:fe697e0cb24a

#! /usr/bin/env python
#
# 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 os
import khmer
from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter

WORKER_THREADS = 8

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_counting_hash(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):