split-fasta.py

#! /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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# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
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#       notice, this list of conditions and the following disclaimer.
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#     * Redistributions in binary form must reproduce the above
#       copyright notice, this list of conditions and the following
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#       with the distribution.
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#     * 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
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# 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,
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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# Contact: khmer-project@idyll.org
import sys
import screed


def main():
    filename = sys.argv[1]
    prefix = sys.argv[2]
    size = int(float(sys.argv[3]))          # e.g. 1e9

    division = -1
    for n, record in enumerate(screed.open(filename)):
        if n % 100000 == 0:
            print('...', n)

        if n % size == 0:
            division += 1
            new_name = '%s.%04d.fa' % (prefix, division)
            print('opening', new_name)
            fp = open(new_name, 'w')

        fp.write('>%s\n%s\n' % (record['name'], record['sequence']))


if __name__ == '__main__':
    main()