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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 """Convert a FASTQ file to a FASTA file"""
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32
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33 import os
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34 import sys
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35 from optparse import OptionParser
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36 from SMART.Java.Python.misc.RPlotter import RPlotter
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37 from SMART.Java.Python.misc.Progress import Progress
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38 from math import *
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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 = "FastQ to FastA v1.0.1: Convert a FastQ file into a FastA file. [Category: Personnal]"
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44
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45 parser = OptionParser(description = description)
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46 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in FASTQ format]")
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47 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in FASTA format]")
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48 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
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49 (options, args) = parser.parse_args()
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50
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51 inputFile = open(options.inputFileName)
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52 outputFastaFile = open(options.outputFileName, "w")
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53
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54 inSequenceName = False
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55 inQualityName = False
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56 inSequence = False
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57 inQuality = True
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58 sequenceName = None
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59 lineNumber = 1
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60
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61 for line in inputFile:
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62
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63 if inSequenceName:
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64 inSequence = True
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65 inSequenceName = False
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66 elif inQualityName:
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67 inQuality = True
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68 inQualityName = False
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69 elif inSequence:
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70 inQualityName = True
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71 inSequence = False
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72 elif inQuality:
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73 inSequenceName = True
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74 inQuality = False
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75 else:
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76 sys.exit("Error! Do not in which section I am (line is %d)" % (lineNumber))
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77
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78 line = line.strip()
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79 if inSequenceName:
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80 if line[0] != "@":
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81 sys.exit("Error! Sequence name '%s' does not start with '@' (line is %d)" % (line, lineNumber))
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82 sequenceName = line[1:]
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83 outputFastaFile.write(">%s\n" % (sequenceName))
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84 elif inQualityName:
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85 if line[0] != "+":
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86 sys.exit("Error! Quality name '%s' does not start with '+' (line is %d)" % (line, lineNumber))
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87 if len(line) > 1 and sequenceName != line[1:]:
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88 sys.exit("Names in sequence and qual are different (%s, %s) (line is %d)" % (sequenceName, line[1:], lineNumber))
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89 elif inSequence:
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90 outputFastaFile.write("%s\n" % (line))
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91 elif inQuality:
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92 pass
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93 lineNumber += 1
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94
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95 inputFile.close()
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96 outputFastaFile.close()
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