Mercurial > repos > dereeper > ragoo
comparison RaGOO/ragoo_utilities/get_contig_borders.py @ 13:b9a3aeb162ab draft default tip
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| author | dereeper |
|---|---|
| date | Mon, 26 Jul 2021 18:22:37 +0000 |
| parents | |
| children |
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| 12:68a9ec9ce51e | 13:b9a3aeb162ab |
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| 1 | |
| 2 if __name__ == "__main__": | |
| 3 import argparse | |
| 4 | |
| 5 parser = argparse.ArgumentParser(description='given and orderings file and a contigs fasta index, print a bed file of contig placements in the pseudomolecules.') | |
| 6 parser.add_argument("orderings", metavar="<orderings.txt>", type=str, help="orderings file from RaGOO") | |
| 7 parser.add_argument("fai", metavar="<contigs.fasta.fai>", type=str, help="index file for contigs (samtools faidx contigs.fasta)") | |
| 8 parser.add_argument("gap_len", metavar="100", type=int, help="Gap size used for pseudomolecule padding.") | |
| 9 | |
| 10 # Get the command line arguments | |
| 11 args = parser.parse_args() | |
| 12 orderings_file = args.orderings | |
| 13 fai_file = args.fai | |
| 14 gap_len = args.gap_len | |
| 15 | |
| 16 # Save the contig orderings | |
| 17 ctgs = [] | |
| 18 with open(orderings_file, 'r') as f: | |
| 19 for line in f: | |
| 20 ctgs.append(line.rstrip().split('\t')[0]) | |
| 21 | |
| 22 # Get contig lengths | |
| 23 ctg_lens = dict() | |
| 24 with open(fai_file, 'r') as f: | |
| 25 for line in f: | |
| 26 L1 = line.split('\t') | |
| 27 ctg_lens[L1[0]] = int(L1[1]) | |
| 28 | |
| 29 # Get contig borders | |
| 30 final_bed = [] | |
| 31 current_pos = 0 | |
| 32 | |
| 33 for ctg in ctgs: | |
| 34 start = current_pos | |
| 35 end = current_pos + ctg_lens[ctg] | |
| 36 current_pos += ctg_lens[ctg] | |
| 37 current_pos += gap_len | |
| 38 pm_header = orderings_file[orderings_file.rfind('/')+1:orderings_file.rfind('_')] + '_RaGOO' | |
| 39 final_bed.append('%s\t%r\t%r' % (pm_header, start, end)) | |
| 40 | |
| 41 print('\n'.join(final_bed)) |