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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 |
