/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 95 lines · 66 code · 8 blank · 21 comment · 23 complexity · 343bf5cd1af92f4bd8b5a1a328d6ce86 MD5 · raw file
- #!/usr/bin/env python
- """
- convert fastqsolexa file to separated sequence and quality files.
- assume each sequence and quality score are contained in one line
- the order should be:
- 1st line: @title_of_seq
- 2nd line: nucleotides
- 3rd line: +title_of_qualityscore (might be skipped)
- 4th line: quality scores
- (in three forms: a. digits, b. ASCII codes, the first char as the coding base, c. ASCII codes without the first char.)
- Usage:
- %python fastqsolexa_to_qual_converter.py <your_fastqsolexa_filename> <output_seq_filename> <output_score_filename>
- """
- import sys, os
- from math import *
- assert sys.version_info[:2] >= ( 2, 4 )
- def stop_err( msg ):
- sys.stderr.write( "%s" % msg )
- sys.exit()
- def __main__():
- infile_name = sys.argv[1]
- outfile_score = open( sys.argv[2], 'w' )
- datatype = sys.argv[3]
- qual_title_startswith = ''
- seq_title_startswith = ''
- default_coding_value = 64
- fastq_block_lines = 0
- for i, line in enumerate( file( infile_name ) ):
- line = line.rstrip()
- if not line or line.startswith( '#' ):
- continue
- fastq_block_lines = ( fastq_block_lines + 1 ) % 4
- line_startswith = line[0:1]
- if fastq_block_lines == 1:
- # first line is @title_of_seq
- if not seq_title_startswith:
- seq_title_startswith = line_startswith
- if line_startswith != seq_title_startswith:
- stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) )
- read_title = line[1:]
- elif fastq_block_lines == 2:
- # second line is nucleotides
- read_length = len( line )
- elif fastq_block_lines == 3:
- # third line is +title_of_qualityscore (might be skipped)
- if not qual_title_startswith:
- qual_title_startswith = line_startswith
- if line_startswith != qual_title_startswith:
- stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) )
- quality_title = line[1:]
- if quality_title and read_title != quality_title:
- stop_err( 'Invalid fastqsolexa format at line %d: sequence title "%s" differes from score title "%s".' % ( i + 1, read_title, quality_title ) )
- if not quality_title:
- outfile_score.write( '>%s\n' % read_title )
- else:
- outfile_score.write( '>%s\n' % line[1:] )
- else:
- # fourth line is quality scores
- qual = ''
- fastq_integer = True
- # peek: ascii or digits?
- val = line.split()[0]
- try:
- check = int( val )
- fastq_integer = True
- except:
- fastq_integer = False
- if fastq_integer: # digits
- qual = line
- else:
- # ascii
- quality_score_length = len( line )
- if quality_score_length == read_length + 1:
- quality_score_startswith = ord( line[0:1] )
- line = line[1:]
- elif quality_score_length == read_length:
- quality_score_startswith = default_coding_value
- else:
- 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 ) )
- for j, char in enumerate( line ):
- score = ord( char ) - quality_score_startswith # 64
- qual = "%s%s " % ( qual, str( score ) )
- outfile_score.write( '%s\n' % qual )
- outfile_score.close()
- if __name__ == "__main__": __main__()