Mercurial > repos > iuc > concoct_extract_fasta_bins
view cut_up_fasta.py @ 2:92a2d9109528 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 77dea70f156d56c83b6851b61dc997d2b344bdc9
author | iuc |
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date | Fri, 01 Jul 2022 14:16:40 +0000 (2022-07-01) |
parents | a04028a8181d |
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#!/usr/bin/env python import argparse import gzip from functools import partial from Bio import SeqIO def cut_up_fasta(input_fasta, chunk_size, overlap, merge_last, output_fasta, output_bed, gzipped): if gzipped: _open = partial(gzip.open, mode='rt') else: _open = open fasta_fh = open(output_fasta, 'w') if output_bed is not None: bed_fh = open(output_bed, 'w') with _open(input_fasta) as input_fh: for record in SeqIO.parse(input_fh, "fasta"): if (not merge_last and len(record.seq) > chunk_size) or (merge_last and len(record.seq) >= 2 * chunk_size): for index, split_seq in enumerate(chunks(record.seq, chunk_size, overlap, merge_last)): fasta_fh.write(f">{record.id}.concoct_part_{index}\n{split_seq}\n") if output_bed is not None: bed_fh.write(f"{record.id}\t{chunk_size * index}\t{chunk_size * index + len(split_seq)}\t{record.id}.concoct_part_{index}\n") else: fasta_fh.write(f">{record.id}.concoct_part_0\n{record.seq}\n") if output_bed is not None: bed_fh.write(f"{record.id}\t0\t{len(record.seq)}\t{record.id}.concoct_part_0\n") if output_bed is not None: bed_fh.close() def chunks(seq, chunk_size, overlap_size, merge_last): # Yield successive chunk_size-sized chunks from seq # with given overlap overlap_size between the chunks. assert chunk_size > overlap_size if merge_last: for i in range(0, len(seq) - chunk_size + 1, chunk_size - overlap_size): yield seq[i:i + chunk_size] if i + chunk_size + chunk_size - overlap_size <= len(seq) else seq[i:] else: for i in range(0, len(seq), chunk_size - overlap_size): yield seq[i:i + chunk_size] parser = argparse.ArgumentParser() parser.add_argument("--input_fasta", action="store", dest="input_fasta", help="Fasta files with contigs") parser.add_argument("--gzipped", action="store_true", dest="gzipped", help="Input file is gzipped") parser.add_argument("--chunk_size", action="store", dest="chunk_size", type=int, help="Chunk size\n") parser.add_argument("--overlap_size", action="store", dest="overlap_size", type=int, help="Overlap size\n") parser.add_argument("--merge_last", default=False, action="store_true", dest="merge_last", help="Concatenate final part to last contig\n") parser.add_argument("--output_bed", action="store", dest="output_bed", default=None, help="BED file to be created with exact regions of the original contigs corresponding to the newly created contigs") parser.add_argument("--output_fasta", action="store", dest="output_fasta", help="Output fasta file with cut contigs") args = parser.parse_args() cut_up_fasta(args.input_fasta, args.chunk_size, args.overlap_size, args.merge_last, args.output_fasta, args.output_bed, args.gzipped)