Mercurial > repos > crusoe > khmer

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

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
author crusoe
date Tue, 07 Jul 2015 11:59:39 -0400
parents 0b238b083f77
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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fe697e0cb24a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
crusoe
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1 #! /usr/bin/env python
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2 #
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fe697e0cb24a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
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3 # This file is part of khmer, https://github.com/dib-lab/khmer/, and is
fe697e0cb24a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
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4 # Copyright (C) Michigan State University, 2009-2015. It is licensed under
fe697e0cb24a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
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5 # the three-clause BSD license; see LICENSE.
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Michael R. Crusoe <mcrusoe@msu.edu>
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6 # Contact: khmer-project@idyll.org
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7 #
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fe697e0cb24a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
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8 from __future__ import print_function
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9 import sys
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10 import os
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11 import khmer
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Michael R. Crusoe <mcrusoe@msu.edu>
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12 from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter
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13
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14 WORKER_THREADS = 8
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15 GROUPSIZE = 100
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16
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Michael R. Crusoe <mcrusoe@msu.edu>
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17 CUTOFF = 50
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18
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19 ###
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21
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22 def main():
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23 counting_ht = sys.argv[1]
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24 infiles = sys.argv[2:]
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25
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fe697e0cb24a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
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26 print('file with ht: %s' % counting_ht)
fe697e0cb24a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
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27 print('-- settings:')
fe697e0cb24a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
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28 print('N THREADS', WORKER_THREADS)
fe697e0cb24a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
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29 print('--')
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30
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31 print('making hashtable')
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32 ht = khmer.load_counting_hash(counting_ht)
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33 K = ht.ksize()
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34
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35 for infile in infiles:
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36 print('filtering', infile)
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Michael R. Crusoe <mcrusoe@msu.edu>
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37 outfile = os.path.basename(infile) + '.below'
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38
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39 outfp = open(outfile, 'w')
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40
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41 def process_fn(record, ht=ht):
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42 name = record['name']
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43 seq = record['sequence']
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44 if 'N' in seq:
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45 return None, None
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46
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47 trim_seq, trim_at = ht.trim_below_abundance(seq, CUTOFF)
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48
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49 if trim_at >= K:
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50 return name, trim_seq
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51
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52 return None, None
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53
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54 tsp = ThreadedSequenceProcessor(process_fn, WORKER_THREADS, GROUPSIZE)
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55
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56 tsp.start(verbose_fasta_iter(infile), outfp)
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57
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58 if __name__ == '__main__':
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59 main()