view profrep_masking.py @ 0:a5f1638b73be draft

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#!/usr/bin/env python3

import argparse
from Bio import SeqIO
from Bio.Seq import MutableSeq
from Bio.Alphabet import generic_dna
import sys


def main(args):
    # Command line arguments
    QUERY = args.query
    MODE = args.mode
    REPEAT_GFF = args.repeat_gff
    MASKED = args.output_masked

    repeats_all = get_indices(REPEAT_GFF)

    if MODE == "lowercase":
        lower_mask(QUERY, repeats_all, MASKED)
    else:
        N_mask(QUERY, repeats_all, MASKED)


def get_indices(REPEAT_GFF):
    '''
	Get indices of repeats from GFF file to mask
	'''
    repeats_all = {}
    with open(REPEAT_GFF, "r") as repeats_gff:
        for line in repeats_gff:
            if not line.startswith("#"):
                seq_id = line.split("\t")[0]
                start_r = line.split("\t")[3]
                end_r = line.split("\t")[4]
                if seq_id in repeats_all.keys():
                    repeats_all[seq_id].append([int(start_r), int(end_r)])
                else:
                    repeats_all[seq_id] = [[int(start_r), int(end_r)]]
    return repeats_all


def lower_mask(QUERY, repeats_all, MASKED):
    allSeqs = list(SeqIO.parse(QUERY, 'fasta'))
    for singleSeq in allSeqs:
        mutable = MutableSeq(str(singleSeq.seq), generic_dna)
        for index in repeats_all[singleSeq.id]:
            for item in range(index[0] - 1, index[1]):
                mutable[item] = mutable[item].lower()
        singleSeq.seq = mutable
    with open(MASKED, "w") as handle:
        SeqIO.write(allSeqs, handle, 'fasta')


def N_mask(QUERY, repeats_all, MASKED):
    allSeqs = list(SeqIO.parse(QUERY, 'fasta'))
    for singleSeq in allSeqs:
        mutable = MutableSeq(str(singleSeq.seq), generic_dna)
        for index in repeats_all[singleSeq.id]:
            for item in range(index[0] - 1, index[1]):
                mutable[item] = "N"
        singleSeq.seq = mutable
    with open(MASKED, "w") as handle:
        SeqIO.write(allSeqs, handle, 'fasta')


if __name__ == "__main__":

    # Command line arguments
    parser = argparse.ArgumentParser()
    parser.add_argument('-q',
                        '--query',
                        type=str,
                        required=True,
                        help='query sequence to be processed')
    parser.add_argument('-rg',
                        '--repeat_gff',
                        type=str,
                        required=True,
                        help='query sequence to be processed')
    parser.add_argument('-m',
                        '--mode',
                        default="lowercase",
                        choices=['lowercase', 'N'],
                        help='query sequence to be processed')
    parser.add_argument('-o',
                        '--output_masked',
                        type=str,
                        default="output_masked",
                        help='query sequence to be processed')

    args = parser.parse_args()
    main(args)