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Source code for galaxy.datatypes.converters.fastqsolexa_to_qual_converter

#!/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

assert sys.version_info[:2] >= ( 2, 4 )


[docs]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( open( 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: 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__()