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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 """Update a .qual file given a .fasta file"""
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32
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33 from optparse import OptionParser
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34 from commons.core.parsing.FastaParser import *
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35 from SMART.Java.Python.misc.Progress import *
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36
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37
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38 if __name__ == "__main__":
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39
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40 # parse command line
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41 description = "Update Qual v1.0.1: Remove the sequence in a Qual file which are not in the corresponding Fasta file. [Category: Personnal]"
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42
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43 parser = OptionParser(description = description)
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44 parser.add_option("-f", "--fasta", dest="fastaFile", action="store", type="string", help="fasta file [compulsory] [format: file in FASTA format]")
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45 parser.add_option("-q", "--qual", dest="qualFile", action="store", type="string", help="qual file [compulsory] [format: file in QUAL format]")
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46 parser.add_option("-o", "--output", dest="outputFile", action="store", type="string", help="output file [compulsory] [format: output file in QUAL format]")
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47 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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48 (options, args) = parser.parse_args()
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49
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50 parser = SequenceListParser(options.fastaFile, options.verbosity)
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51 nbSequences = parser.getNbSequences()
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52 progress = Progress(nbSequences, "Parsing file %s" % (options.fastaFile), options.verbosity)
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53 qualHandle = open(options.qualFile)
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54 outputHandle = open(options.outputFile, "w")
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55 nbRefused = 0
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56 nbTotal = 0
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57
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58 names = []
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59 while parser.getNextSequence():
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60 sequence = parser.getCurrentSequence()
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61 nbTotal += 1
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62
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63 found = False
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64 name = None
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65 for line in qualHandle:
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66 line = line.strip()
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67 if line[0] == ">":
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68 name = line[1:]
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69 if name == sequence.name:
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70 found = True
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71 else:
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72 nbRefused += 1
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73 else:
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74 if found:
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75 outputHandle.write(">%s\n%s\n" % (name, line))
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76 found = False
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77 name = None
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78 break
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79 progress.inc()
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80 progress.done()
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81
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82
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83 outputHandle.close()
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84 qualHandle.close()
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85
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86 print "%d out of %d are refused (%f%%)" % (nbRefused, nbTotal, (float(nbRefused) / nbTotal * 100))
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