#!/usr/bin/env python

import os
from optparse import OptionParser
import numpy
import sys

def qseq2fastq(destination, qseqs, trim=None, pf=False):
    for q in qseqs:
        for line in open(q):
            # parse line
            record = line.strip().split('\t')
            machine_name = record[0]
            run_number = record[1]
            lane_number = record[2]
            tile = record[3]
            x = record[4]
            y = record[5]
            index = record[6]
            read = record[7]
            sequence = record[8].replace('.','N')
            # Illumina scores are Phred + 64
            # Fastq scores are Phread + 33
            # the following code grabs the string, converts to short ints and
            # subtracts 31 (64-33) to convert between the two score formats.
            # The numpy solution is twice as fast as some of my other
            # ideas for the conversion.
            # sorry about the uglyness in changing from character, to 8-bit int
            # and back to a character array
            quality = numpy.asarray(record[9],'c')
            quality.dtype = numpy.uint8
            quality -= 31
            quality.dtype = '|S1' # I'd like to know what the real numpy char type is

            if pf:
                pass_qc = record[10]
                pass_qc_msg = " pf=%s" % (pass_qc)
            else:
                pass_qc_msg = ""
                
            destination.write('@%s_%s:%s:%s:%s:%s/%s%s%s' % ( \
                machine_name,
                run_number,
                lane_number,
                tile,
                x,
                y,
                read,
                pass_qc_msg,
                os.linesep))
            destination.write(sequence[trim])
            destination.write(os.linesep)
            destination.write('+')
            destination.write(os.linesep)
            destination.write(quality[trim].tostring())
            destination.write(os.linesep)

def make_parser():
    usage = "%prog: [options] *_qseq.txt"
    parser = OptionParser(usage)
    parser.add_option('-o', '--output', help='output fastq file', default=None)
    parser.add_option('-s', '--slice',
                      help='specify python slice, e.g. 0:75, 0:-1',
                      default=None)
    parser.add_option('--pf', help="report pass filter flag", default=False,
                      action="store_true")
    return parser

def parse_slice(slice_text):
    if slice_text is None or len(slice_text) == 0:
        return slice(None)
        
    slice_data = []
    for element in slice_text.split(':'):
        if len(element) == 0:
            element = None
        else:
            element = int(element)
        slice_data.append(element)

    return slice(*slice_data)
        

def main(cmdline=None):
    parser = make_parser()
    opts, args = parser.parse_args(cmdline)

    if opts.output is not None:
        dest = open(opts.output, 'w')
    else:
        dest = sys.stdout

    subseq = parse_slice(opts.slice)

    qseq2fastq(dest, args, subseq, opts.pf)
    
    return 0

if __name__ == "__main__":
    main()