Mercurial > repos > iuc > khmer_abundance_distribution

annotate filter-below-abund.py @ 9:7624945cacd3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 11:47:51 +0000
parents 5a97c5bbd51e
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c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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1 #! /usr/bin/env python
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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2 # This file is part of khmer, https://github.com/dib-lab/khmer/, and is
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3 # Copyright (C) 2011-2015, Michigan State University.
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4 # Copyright (C) 2015, The Regents of the University of California.
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5 #
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6 # Redistribution and use in source and binary forms, with or without
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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7 # modification, are permitted provided that the following conditions are
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8 # met:
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9 #
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10 # * Redistributions of source code must retain the above copyright
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11 # notice, this list of conditions and the following disclaimer.
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12 #
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13 # * Redistributions in binary form must reproduce the above
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14 # copyright notice, this list of conditions and the following
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15 # disclaimer in the documentation and/or other materials provided
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16 # with the distribution.
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17 #
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18 # * Neither the name of the Michigan State University nor the names
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19 # of its contributors may be used to endorse or promote products
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20 # derived from this software without specific prior written
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21 # permission.
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22 #
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23 # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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24 # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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25 # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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26 # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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27 # HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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28 # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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29 # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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30 # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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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
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37
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38 import os
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39 import sys
5
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40
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41 import screed
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42 from khmer import Countgraph, ReadParser
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43 from khmer.utils import (broken_paired_reader, write_record)
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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 def main():
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49 counting_ht = sys.argv[1]
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50 infiles = sys.argv[2:]
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51
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52 print('file with ht: %s' % counting_ht)
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53
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54 print('making hashtable')
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55 ht = Countgraph.load(counting_ht)
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56 K = ht.ksize()
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57
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58 for infile in infiles:
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59 print('filtering', infile)
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60 outfile = os.path.basename(infile) + '.below'
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61
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62 outfp = open(outfile, 'w')
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63
6
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64 paired_iter = broken_paired_reader(ReadParser(infile), min_length=K,
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65 force_single=True)
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66 for n, is_pair, read1, read2 in paired_iter:
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67 name = read1.name
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68 seq = read1.sequence
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69 if 'N' in seq:
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70 return None, None
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71
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72 trim_seq, trim_at = ht.trim_below_abundance(seq, CUTOFF)
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73
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74 if trim_at >= K:
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75 write_record(screed.Record(name=name, sequence=trim_seq), outfp)
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76
4
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77
0
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78 if __name__ == '__main__':
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79 main()