annotate gff_selection.py @ 5:ad3bbf392135 draft

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#!/usr/bin/env python3

import argparse


def check_file_start(gff_file):
    count_comment = 0
    with open(gff_file, "r") as gff_all:
        line = gff_all.readline()
        while line.startswith("#"):
            line = gff_all.readline()
            count_comment += 1
    return count_comment


def cut_region(GFF_IN, GFF_OUT, REGION, NEW_SEQ_ID):
    '''
	Extract records for particular sequence and/or region from arbitrary GFF3 file
	in form: original_seq_name:start-end (e.g. chr1:1000-2000)
	Write a new GFF containing only records from this region
	If new SEQ ID for extracted region is not provided, it will be named based on the region to cut
	! ALLOWS TO CUT ONLY ONE REGION AT A TIME
	'''
    ## cut a particular part of a paritcular sequence
    if ":" and "-" in REGION:
        seq_to_cut = ":".join(REGION.split(":")[:-1])
        int_start = int(REGION.split(":")[-1].split("-")[0])
        int_end = int(REGION.split(":")[-1].split("-")[1])
    ## cut the whole sequence if region is not specified
    else:
        int_start = 0
        int_end = float("inf")
        seq_to_cut = REGION
    count_comment = check_file_start(GFF_IN)
    with open(GFF_OUT, "w") as gff_out:
        with open(GFF_IN, "r") as gff_in:
            for comment_idx in range(count_comment):
                next(gff_in)
            gff_out.write("##gff-version 3\n")
            gff_out.write("##sequence region {}\n".format(REGION))
            for line in gff_in:
                if not line.startswith("#") and line.split("\t")[
                        0] == seq_to_cut and int(float(line.split("\t")[
                            3])) >= int_start and int(float(line.split("\t")[
                                4])) <= int_end:
                    new_start = int(line.split("\t")[3]) - int_start + 1
                    new_end = int(line.split("\t")[4]) - int_start + 1
                    gff_out.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}".format(
                        NEW_SEQ_ID, line.split("\t")[1], line.split("\t")[
                            2], new_start, new_end, line.split("\t")[
                                5], line.split("\t")[6], line.split("\t")[
                                    7], line.split("\t")[8]))


def main(args):
    # Command line arguments
    GFF_IN = args.gff_input
    GFF_OUT = args.gff_output
    REGION = args.region
    NEW_SEQ_ID = args.new_seq_id

    if GFF_OUT is None:
        GFF_OUT = "{}_cut{}.gff3".format(GFF_IN, REGION)

    if not NEW_SEQ_ID:
        NEW_SEQ_ID = REGION

    cut_region(GFF_IN, GFF_OUT, REGION, NEW_SEQ_ID)


if __name__ == "__main__":

    # Command line arguments
    parser = argparse.ArgumentParser()
    parser.add_argument('-gi',
                        '--gff_input',
                        type=str,
                        required=True,
                        help='choose gff file')
    parser.add_argument(
        '-go', '--gff_output',
        type=str, help='choose gff file')
    parser.add_argument('-si', '--new_seq_id', type=str, help=' ')
    parser.add_argument('-rg', '--region', type=str, required=True, help=' ')
    args = parser.parse_args()
    main(args)