1 | #!/usr/bin/env python |
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2 | |
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3 | """ |
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4 | convert fastqsolexa file to separated sequence and quality files. |
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5 | |
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6 | assume each sequence and quality score are contained in one line |
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7 | the order should be: |
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8 | 1st line: @title_of_seq |
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9 | 2nd line: nucleotides |
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10 | 3rd line: +title_of_qualityscore (might be skipped) |
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11 | 4th line: quality scores |
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12 | (in three forms: a. digits, b. ASCII codes, the first char as the coding base, c. ASCII codes without the first char.) |
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13 | |
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14 | Usage: |
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15 | %python fastqsolexa_to_fasta_qual.py <your_fastqsolexa_filename> <output_seq_filename> <output_score_filename> |
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16 | """ |
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17 | |
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18 | import sys, os |
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19 | from math import * |
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20 | |
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21 | assert sys.version_info[:2] >= ( 2, 4 ) |
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22 | |
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23 | def stop_err( msg ): |
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24 | sys.stderr.write( "%s" % msg ) |
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25 | sys.exit() |
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26 | |
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27 | def __main__(): |
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28 | infile_name = sys.argv[1] |
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29 | outfile_seq = open( sys.argv[2], 'w' ) |
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30 | outfile_score = open( sys.argv[3], 'w' ) |
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31 | datatype = sys.argv[4] |
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32 | seq_title_startswith = '' |
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33 | qual_title_startswith = '' |
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34 | default_coding_value = 64 |
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35 | fastq_block_lines = 0 |
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36 | |
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37 | for i, line in enumerate( file( infile_name ) ): |
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38 | line = line.rstrip() |
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39 | if not line or line.startswith( '#' ): |
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40 | continue |
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41 | fastq_block_lines = ( fastq_block_lines + 1 ) % 4 |
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42 | line_startswith = line[0:1] |
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43 | if fastq_block_lines == 1: |
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44 | # first line is @title_of_seq |
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45 | if not seq_title_startswith: |
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46 | seq_title_startswith = line_startswith |
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47 | if line_startswith != seq_title_startswith: |
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48 | outfile_seq.close() |
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49 | outfile_score.close() |
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50 | stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) ) |
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51 | read_title = line[1:] |
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52 | outfile_seq.write( '>%s\n' % line[1:] ) |
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53 | elif fastq_block_lines == 2: |
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54 | # second line is nucleotides |
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55 | read_length = len( line ) |
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56 | outfile_seq.write( '%s\n' % line ) |
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57 | elif fastq_block_lines == 3: |
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58 | # third line is +title_of_qualityscore ( might be skipped ) |
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59 | if not qual_title_startswith: |
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60 | qual_title_startswith = line_startswith |
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61 | if line_startswith != qual_title_startswith: |
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62 | outfile_seq.close() |
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63 | outfile_score.close() |
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64 | stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) ) |
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65 | quality_title = line[1:] |
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66 | if quality_title and read_title != quality_title: |
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67 | outfile_seq.close() |
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68 | outfile_score.close() |
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69 | stop_err( 'Invalid fastqsolexa format at line %d: sequence title "%s" differes from score title "%s".' % ( i + 1, read_title, quality_title ) ) |
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70 | if not quality_title: |
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71 | outfile_score.write( '>%s\n' % read_title ) |
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72 | else: |
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73 | outfile_score.write( '>%s\n' % line[1:] ) |
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74 | else: |
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75 | # fourth line is quality scores |
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76 | qual = '' |
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77 | fastq_integer = True |
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78 | # peek: ascii or digits? |
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79 | val = line.split()[0] |
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80 | try: |
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81 | check = int( val ) |
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82 | fastq_integer = True |
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83 | except: |
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84 | fastq_integer = False |
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85 | |
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86 | if fastq_integer: |
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87 | # digits |
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88 | qual = line |
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89 | else: |
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90 | # ascii |
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91 | quality_score_length = len( line ) |
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92 | if quality_score_length == read_length + 1: |
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93 | # first char is qual_score_startswith |
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94 | qual_score_startswith = ord( line[0:1] ) |
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95 | line = line[1:] |
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96 | elif quality_score_length == read_length: |
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97 | qual_score_startswith = default_coding_value |
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98 | else: |
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99 | stop_err( 'Invalid fastqsolexa format at line %d: the number of quality scores ( %d ) is not the same as bases ( %d ).' % ( i + 1, quality_score_length, read_length ) ) |
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100 | for j, char in enumerate( line ): |
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101 | score = ord( char ) - qual_score_startswith # 64 |
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102 | qual = "%s%s " % ( qual, str( score ) ) |
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103 | outfile_score.write( '%s\n' % qual ) |
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104 | |
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105 | outfile_seq.close() |
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106 | outfile_score.close() |
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107 | |
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108 | if __name__ == "__main__": __main__() |
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109 | |
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