#!/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_fasta_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 = open( sys.argv[2], 'w' )
    fastq_block_lines = 0
    seq_title_startswith = ''

    for i, line in enumerate( file( infile_name ) ):
        line = line.rstrip() # eliminate trailing space and new line characters
        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:
            # line 1 is sequence title
            if not seq_title_startswith:
                seq_title_startswith = line_startswith
            if seq_title_startswith != line_startswith:
                stop_err( 'Invalid fastqsolexa format at line %d: %s.' %( i + 1, line ) )
            read_title = line[ 1: ]
            outfile.write( '>%s\n' % line[1:] )
        elif fastq_block_lines == 2:
            # line 2 is nucleotides
            read_length = len( line )
            outfile.write( '%s\n' % line )
        else:
            pass

    outfile.close()

if __name__ == "__main__": __main__()