Chorus2/ChorusNGSselect.py at master · ljq12697/Chorus2 · GitHub

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import sys
import argparse
import os
import pandas as pd
from Choruslib.revcom import revcom

def main():

    args = check_options(get_options())


    try:

        probe = pd.read_table(args.input,names=("chrom","start","end","sequence","score","strand"),
                      dtype={"chrom":str,"start":int,"end":int,"sequence":str,"score":int,"strand":str})

        ftprobe = probe[((probe.score > args.mink) & (probe.score < args.maxk) & (
                    probe.score > probe.score.quantile(args.minquantile)) & (
                                 probe.score < probe.score.quantile(args.maxquantile)))]

        probe = ''

        chromnames = ftprobe.chrom.unique()

        outio = open(args.output, 'w')

        for chrom in chromnames:

            prestart = 0

            strandfr = 1

            for index, row in ftprobe[ftprobe.chrom == chrom].sort_values(by='start').iterrows():

                nowpbstart = row.start

                if nowpbstart > prestart + args.dis:

                    if args.strand == True:

                        if strandfr % 2 == 0:
                            row[5] = '-'
                            row[3] = revcom(row[3])

                    strandfr += 1

                    prestart = nowpbstart

                    print(row.chrom, row.start, row.end, row.sequence, row.score, row.strand, sep='\t', file=outio)

        outio.close()

        print("Filtered finished!")

    except:

        print("Probe file format error. Please check your probe file!")

        sys.exit(1)


def check_options(parser):

    args = parser.parse_args()

    if args.input:

        if not os.path.exists(args.input):

            print("Can not locate input file, please input input file.\n")

            parser.print_help()

            sys.exit(1)

    if args.mink > args.maxk:

        print("min k-mer (%s) score greater than max k-mer (%s) score" % (args.mink , args.maxk))

        parser.print_help()

        sys.exit(1)


    if args.minquantile > args.maxquantile:

        print("min quantile (%s) greater than max quantile (%s)" % (args.minquantile , args.maxquantile))

        parser.print_help()

        sys.exit(1)

    if args.minquantile > 1 or args.minquantile < 0:

        print("min quantile error, please check!")

        parser.print_help()

        sys.exit(1)

    if args.maxquantile > 1 or args.maxquantile < 0:

        print("max quantile error, please check!")

        parser.print_help()

        sys.exit(1)

    return args


def get_options():

    parser = argparse.ArgumentParser(description="ChorusNGSselect for Oligo FISH probe selection by NGS k-mer score", prog='ChorusNGSselect',
                                     formatter_class=argparse.RawDescriptionHelpFormatter,
                                     epilog="Example:\n"
                                            "  ChorusNGSselect -i ChorusNGSfilter_output.bed -q 0.1 -p 0.9 -d 25 \\ \n"
                                            "                  -o filtered_output.bed"
                                     )

    parser.add_argument('--version', action='version', version='%(prog)s 1.0')

    parser.add_argument('-i', '--input', dest='input', help='Input bed format probe file generated by ChorusNGSfilter',
                        required=True, type=str)

    parser.add_argument('-o', '--output', dest='output', help='Output bed format probe file after k-mer score filter. (Default: filtered_output.bed)',
                        default='filtered_output.bed', type=str)

    parser.add_argument('-m', '--min', dest='mink', help='Minimum k-mer score, score < min value will be dropped. For example: 900. '
                             'Incompatible with parameter \'-q/-p\' (Default: 0)', default=0, type=int)

    parser.add_argument('-l', '--max', dest='maxk', help='Maximum k-mer score, score > max value will be dropped. For example: 2000. '
                             'Incompatible with parameter \'-q/-p\' (Default: 10000000)', default=10000000, type=int)

    parser.add_argument('-q', '--minquantile', dest='minquantile', type=float,
                        help='Filter < min%% quantile k-mer score, range from 0 to 1. For example: 0.25 means 25%% quantile. '
                             'Incompatible with parameter \'-m/-l\'. (Default: 0.1)', default=0.1)

    parser.add_argument('-p', '--maxquantile', dest='maxquantile', type=float,
                        help='Filter > max%% quantile k-mer score, range from 0 to 1. For example: 0.75 means 75%% quantile. '
                             'Incompatible with parameter \'-m/-l\'. (Default: 0.9)', default=0.9)

    parser.add_argument('-bs', '--bothstrand', dest='strand', help='Keep both + and - strand probes. (Default is True)',
                        action='store_true')

    parser.add_argument('-ss', '--singlestrand', dest='strand', help='Keep only + strand probes. Incompatible with parameter \'-bs/--bothstrand\'',
                        action='store_false')

    parser.set_defaults(strand=True)

    parser.add_argument('-d', '--distance', dest='dis', help='Minimum distance between two adjacent probes. (Default: 25)',
                        default=25, type=int)

    return parser


if __name__ == "__main__":

    try:

        main()

    except KeyboardInterrupt:

        sys.stderr.write("User interrupt\n")

        sys.exit(0)