Mercurial > repos > iuc > khmer

annotate filter-below-abund.py @ 0:0187f18785a3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
author iuc
date Sat, 17 Oct 2015 04:02:33 -0400
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0
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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1 #! /usr/bin/env python
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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2 # This file is part of khmer, https://github.com/dib-lab/khmer/, and is
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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3 # Copyright (C) 2011-2015, Michigan State University.
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iuc
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4 # Copyright (C) 2015, The Regents of the University of California.
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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5 #
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iuc
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6 # Redistribution and use in source and binary forms, with or without
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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7 # modification, are permitted provided that the following conditions are
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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8 # met:
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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9 #
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iuc
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10 # * Redistributions of source code must retain the above copyright
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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11 # notice, this list of conditions and the following disclaimer.
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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12 #
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iuc
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13 # * Redistributions in binary form must reproduce the above
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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14 # copyright notice, this list of conditions and the following
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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15 # disclaimer in the documentation and/or other materials provided
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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16 # with the distribution.
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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17 #
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18 # * Neither the name of the Michigan State University nor the names
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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19 # of its contributors may be used to endorse or promote products
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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20 # derived from this software without specific prior written
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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21 # permission.
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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22 #
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23 # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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24 # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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25 # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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26 # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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27 # HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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28 # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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29 # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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30 # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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31 # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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32 # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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33 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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34 #
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35 # Contact: khmer-project@idyll.org
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36 from __future__ import print_function
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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37 import sys
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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38 import os
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39 import khmer
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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40 from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter
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41
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42 WORKER_THREADS = 8
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43 GROUPSIZE = 100
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44
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45 CUTOFF = 50
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46
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47 ###
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48
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49
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50 def main():
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51 counting_ht = sys.argv[1]
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52 infiles = sys.argv[2:]
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53
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54 print('file with ht: %s' % counting_ht)
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55 print('-- settings:')
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56 print('N THREADS', WORKER_THREADS)
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57 print('--')
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58
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59 print('making hashtable')
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60 ht = khmer.load_countgraph(counting_ht)
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61 K = ht.ksize()
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62
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63 for infile in infiles:
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64 print('filtering', infile)
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65 outfile = os.path.basename(infile) + '.below'
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66
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67 outfp = open(outfile, 'w')
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68
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69 def process_fn(record, ht=ht):
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70 name = record['name']
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71 seq = record['sequence']
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72 if 'N' in seq:
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73 return None, None
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74
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75 trim_seq, trim_at = ht.trim_below_abundance(seq, CUTOFF)
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76
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77 if trim_at >= K:
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78 return name, trim_seq
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79
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80 return None, None
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81
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82 tsp = ThreadedSequenceProcessor(process_fn, WORKER_THREADS, GROUPSIZE)
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83
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84 tsp.start(verbose_fasta_iter(infile), outfp)
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85
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86 if __name__ == '__main__':
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87 main()