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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 import sys
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32 from optparse import OptionParser
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33 from commons.core.parsing.SequenceListParser import SequenceListParser
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34 from SMART.Java.Python.misc.Progress import Progress
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35
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36 """
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37 Transform qual and fasta files to a single fastq file
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38 """
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39
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40 if __name__ == "__main__":
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41
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42 # parse command line
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43 description = "Qual To FastQ v1.0.2: Convert a file in FASTA/Qual format to FastQ format. [Category: Conversion]"
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44
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45 parser = OptionParser(description = description)
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46 parser.add_option("-f", "--fasta", dest="fastaFileName", action="store", type="string", help="input fasta file [compulsory] [format: file in FASTA format]")
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47 parser.add_option("-q", "--qual", dest="qualFileName", action="store", type="string", help="input qual file [compulsory] [format: file in TXT format]")
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48 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [compulsory] [format: output file in FASTQ format]")
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49 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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50 (options, args) = parser.parse_args()
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51
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52 fastaFile = open(options.fastaFileName)
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53 qualFile = open(options.qualFileName)
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54 fastqFile = open(options.outputFileName, "w")
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55
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56 fastaLine = fastaFile.readline().strip()
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57 qualLine = qualFile.readline().strip()
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58 header = None
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59 cpt = 0
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60 while fastaLine:
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61 if not qualLine:
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62 raise Exception("Qual file is shorter!")
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63 if fastaLine[0] == ">":
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64 header = fastaLine[1:]
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65 if qualLine[0] != ">":
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66 raise Exception("Discrepencies around %s!" % (header))
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67 fastqFile.write("@%s\n" % (header))
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68 else:
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69 if qualLine[0] == ">":
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70 raise Exception("Discrepencies around %s!" % (qualLine[1:]))
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71 intQualities = qualLine.split()
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72 if len(intQualities) != len(fastaLine):
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73 raise Exception("Sizes of read and quality diverge in %s!" % (header))
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74 chrQualities = [chr(min(int(quality), 93) + 33) for quality in intQualities]
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75 fastqFile.write("%s\n+\n%s\n" % (fastaLine, "".join(chrQualities)))
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76 fastaLine = fastaFile.readline().strip()
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77 qualLine = qualFile.readline().strip()
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78 if cpt % 1000 == 0 and options.verbosity > 1:
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79 sys.stdout.write("%d lines read\r" % (cpt))
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80 sys.stdout.flush()
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81 cpt += 1
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82 if options.verbosity > 0:
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83 print "%d lines read" % (cpt)
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84
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85 if qualLine:
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86 raise Exception("Qual file is longer!")
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87
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