#!/usr/bin/env python

"""
Converts SOLiD data to Sanger FASTQ format.

usage: %prog [options]
   -i, --input1=i: Forward reads file
   -q, --input2=q: Forward qual file
   -I, --input3=I: Reverse reads file
   -Q, --input4=Q: Reverse qual file
   -o, --output1=o: Forward output
   -r, --output2=r: Reverse output

usage: %prog forward_reads_file forwards_qual_file reverse_reads_file(or_None) reverse_qual_file(or_None) output_file ouptut_id output_dir
"""

import os
import sys
import tempfile

from bx.cookbook import doc_optparse


def stop_err(msg):
    sys.stderr.write("%s\n" % msg)
    sys.exit()


def replaceNeg1(fin, fout):
    line = fin.readline()
    while line.strip():
        fout.write(line.replace("-1", "1"))
        line = fin.readline()
    fout.seek(0)
    return fout


def __main__():
    # Parse Command Line
    options, args = doc_optparse.parse(__doc__)
    # common temp file setup
    tmpf = tempfile.NamedTemporaryFile()  # forward reads
    tmpqf = tempfile.NamedTemporaryFile()
    tmpqf = replaceNeg1(open(options.input2), tmpqf)
    # if paired-end data (have reverse input files)
    if options.input3 != "None" and options.input4 != "None":
        tmpr = tempfile.NamedTemporaryFile()  # reverse reads
        # replace the -1 in the qualities file
        tmpqr = tempfile.NamedTemporaryFile()
        tmpqr = replaceNeg1(open(options.input4, "r"), tmpqr)
        cmd1 = "%s/bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s 2>&1" % (
            os.path.split(sys.argv[0])[0],
            tmpf.name,
            tmpr.name,
            options.input1,
            tmpqf.name,
            options.input3,
            tmpqr.name,
        )
        try:
            os.system(cmd1)
            os.system("gunzip -c %s >> %s" % (tmpf.name, options.output1))
            os.system("gunzip -c %s >> %s" % (tmpr.name, options.output2))
        except Exception as eq:
            stop_err("Error converting data to fastq format.\n" + str(eq))
        tmpr.close()
        tmpqr.close()
    # if single-end data
    else:
        cmd1 = "%s/bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s 2>&1" % (
            os.path.split(sys.argv[0])[0],
            tmpf.name,
            None,
            options.input1,
            tmpqf.name,
            None,
            None,
        )
        try:
            os.system(cmd1)
            os.system("gunzip -c %s >> %s" % (tmpf.name, options.output1))
        except Exception as eq:
            stop_err("Error converting data to fastq format.\n" + str(eq))
    tmpqf.close()
    tmpf.close()
    sys.stdout.write("converted SOLiD data")


if __name__ == "__main__":
    __main__()