#!/usr/bin/env python
# This code exists in 2 places: ~/datatypes/converters and ~/tools/filters

import sys

assert sys.version_info[:2] >= (2, 6)


def __main__():
    input_name = sys.argv[1]
    output_name = sys.argv[2]
    skipped_lines = 0
    first_skipped_line = 0
    i = 0
    with open(input_name) as fh, open(output_name, 'w') as out:
        out.write("##gff-version 2\n")
        out.write("##bed_to_gff_converter.py\n\n")
        for i, line in enumerate(fh):
            complete_bed = False
            line = line.rstrip('\r\n')
            if line and not line.startswith('#') and not line.startswith('track') and not line.startswith('browser'):
                try:
                    elems = line.split('\t')
                    if len(elems) == 12:
                        complete_bed = True
                    chrom = elems[0]
                    if complete_bed:
                        feature = "mRNA"
                    else:
                        try:
                            feature = elems[3]
                        except Exception:
                            feature = 'feature%d' % (i + 1)
                    start = int(elems[1]) + 1
                    end = int(elems[2])
                    try:
                        score = elems[4]
                    except Exception:
                        score = '0'
                    try:
                        strand = elems[5]
                    except Exception:
                        strand = '+'
                    try:
                        group = elems[3]
                    except Exception:
                        group = 'group%d' % (i + 1)
                    if complete_bed:
                        out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s %s;\n' % (chrom, feature, start, end, score, strand, feature, group))
                    else:
                        out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s;\n' % (chrom, feature, start, end, score, strand, group))
                    if complete_bed:
                        # We have all the info necessary to annotate exons for genes and mRNAs
                        block_count = int(elems[9])
                        block_sizes = elems[10].split(',')
                        block_starts = elems[11].split(',')
                        for j in range(block_count):
                            exon_start = int(start) + int(block_starts[j])
                            exon_end = exon_start + int(block_sizes[j]) - 1
                            out.write('%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\texon %s;\n' % (chrom, exon_start, exon_end, score, strand, group))
                except Exception:
                    skipped_lines += 1
                    if not first_skipped_line:
                        first_skipped_line = i + 1
            else:
                skipped_lines += 1
                if not first_skipped_line:
                    first_skipped_line = i + 1
    info_msg = "%i lines converted to GFF version 2.  " % (i + 1 - skipped_lines)
    if skipped_lines > 0:
        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % (skipped_lines, first_skipped_line)
    print(info_msg)


if __name__ == "__main__":
    __main__()
