view filter-below-abund.py @ 6:2c763fb18010 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"

#! /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.
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from __future__ import print_function

import os
import sys

import screed
from khmer import Countgraph, ReadParser
from khmer.utils import (broken_paired_reader, write_record)

CUTOFF = 50


def main():
    counting_ht = sys.argv[1]
    infiles = sys.argv[2:]

    print('file with ht: %s' % counting_ht)

    print('making hashtable')
    ht = Countgraph.load(counting_ht)
    K = ht.ksize()

    for infile in infiles:
        print('filtering', infile)
        outfile = os.path.basename(infile) + '.below'

        outfp = open(outfile, 'w')

        paired_iter = broken_paired_reader(ReadParser(infile), min_length=K,
                                           force_single=True)
        for n, is_pair, read1, read2 in paired_iter:
            name = read1.name
            seq = read1.sequence
            if 'N' in seq:
                return None, None

            trim_seq, trim_at = ht.trim_below_abundance(seq, CUTOFF)

            if trim_at >= K:
                write_record(screed.Record(name=name, sequence=trim_seq), outfp)


if __name__ == '__main__':
    main()