root/galaxy-central/tools/metag_tools/fastqsolexa_to_fasta_qual.py @ 2

リビジョン 2, 4.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1#!/usr/bin/env python
2
3"""
4convert fastqsolexa file to separated sequence and quality files.
5
6assume each sequence and quality score are contained in one line
7the order should be:
81st line: @title_of_seq
92nd line: nucleotides
103rd line: +title_of_qualityscore (might be skipped)
114th line: quality scores
12(in three forms: a. digits, b. ASCII codes, the first char as the coding base, c. ASCII codes without the first char.)
13
14Usage:
15%python fastqsolexa_to_fasta_qual.py <your_fastqsolexa_filename> <output_seq_filename> <output_score_filename>
16"""
17
18import sys, os
19from math import *
20
21assert sys.version_info[:2] >= ( 2, 4 )
22
23def stop_err( msg ):
24    sys.stderr.write( "%s" % msg )
25    sys.exit()
26
27def __main__():
28    infile_name = sys.argv[1]
29    outfile_seq = open( sys.argv[2], 'w' )
30    outfile_score = open( sys.argv[3], 'w' )
31    datatype = sys.argv[4]
32    seq_title_startswith = ''
33    qual_title_startswith = ''
34    default_coding_value = 64
35    fastq_block_lines = 0
36   
37    for i, line in enumerate( file( infile_name ) ):
38        line = line.rstrip()
39        if not line or line.startswith( '#' ):
40            continue
41        fastq_block_lines = ( fastq_block_lines + 1 ) % 4
42        line_startswith = line[0:1]
43        if fastq_block_lines == 1:
44            # first line is @title_of_seq
45            if not seq_title_startswith:
46                seq_title_startswith = line_startswith
47            if line_startswith != seq_title_startswith:
48                outfile_seq.close()
49                outfile_score.close()
50                stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) )
51            read_title = line[1:]
52            outfile_seq.write( '>%s\n' % line[1:] )
53        elif fastq_block_lines == 2:
54            # second line is nucleotides
55            read_length = len( line )
56            outfile_seq.write( '%s\n' % line )
57        elif fastq_block_lines == 3:
58            # third line is +title_of_qualityscore ( might be skipped )
59            if not qual_title_startswith:
60                qual_title_startswith = line_startswith
61            if line_startswith != qual_title_startswith:
62                outfile_seq.close()
63                outfile_score.close()
64                stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) )   
65            quality_title = line[1:]
66            if quality_title and read_title != quality_title:
67                outfile_seq.close()
68                outfile_score.close()
69                stop_err( 'Invalid fastqsolexa format at line %d: sequence title "%s" differes from score title "%s".' % ( i + 1, read_title, quality_title ) )
70            if not quality_title:
71                outfile_score.write( '>%s\n' % read_title )
72            else:
73                outfile_score.write( '>%s\n' % line[1:] )
74        else:
75            # fourth line is quality scores
76            qual = ''
77            fastq_integer = True
78            # peek: ascii or digits?
79            val = line.split()[0]
80            try:
81                check = int( val )
82                fastq_integer = True
83            except:
84                fastq_integer = False
85               
86            if fastq_integer:
87                # digits
88                qual = line
89            else:
90                # ascii
91                quality_score_length = len( line )
92                if quality_score_length == read_length + 1:
93                    # first char is qual_score_startswith
94                    qual_score_startswith = ord( line[0:1] )
95                    line = line[1:]
96                elif quality_score_length == read_length:
97                    qual_score_startswith = default_coding_value
98                else:
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 ) )
100                for j, char in enumerate( line ):
101                    score = ord( char ) - qual_score_startswith    # 64
102                    qual = "%s%s " % ( qual, str( score ) )
103            outfile_score.write( '%s\n' % qual )
104             
105    outfile_seq.close()
106    outfile_score.close()
107
108if __name__ == "__main__": __main__()
109   
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