annotate SAR_finder.py @ 2:373c8bca8a82 draft default tip

planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc

import sys
import argparse
import os
import re
from biopython_parsing import FASTA_parser
from file_operations import fasta_from_SAR_dict, gff3_from_SAR_dict, tab_from_SAR_dict
from SAR_functions import CheckSequence

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="SAR Finder")

    parser.add_argument(
        "fa", type=argparse.FileType("r"), help="organism's multi fasta file"
    )

    parser.add_argument(
        "--min", type=int, default=20, help="minimum size of candidate peptide"
    )

    parser.add_argument(
        "--max", type=int, default=200, help="maximum size of candidate peptide"
    )

    parser.add_argument(
        "--sar_min",
        type=int,
        default=15,
        help="minimum size of candidate peptide TMD domain",
    )

    parser.add_argument(
        "--sar_max",
        type=int,
        default=24,
        help="maximum size of candidate peptide TMD domain",
    )

    parser.add_argument(
        "--out_fa",
        type=argparse.FileType("w"),
        help="multifasta output of candidate SAR proteins",
        default="candidate_SAR.fa",
    )

    parser.add_argument(
        "--out_stat",
        type=argparse.FileType("w"),
        help="summary statistic file for candidate SAR proteins, tab separated",
        default="candidate_SAR_stats.tsv",
    )

    parser.add_argument(
        "--out_gff3",
        type=argparse.FileType("w"),
        help="multigff3 file for candidate SAR proteins",
        default="candidate_SAR.gff3",
    )

    args = parser.parse_args()

    fa_dict = FASTA_parser(fa=args.fa).multifasta_dict()

    sars = {}

    for protein_name, protein_data in fa_dict.items():
        sar = CheckSequence(protein_name, protein_data)
        # sar.check_sizes(min=args.min,max=args.max)
        hydros = sar.shrink_results(sar_min=args.sar_min, sar_max=args.sar_max)
        sars.update(hydros)

    gff3_from_SAR_dict(sars, args.out_gff3)
    tab_from_SAR_dict(
        sars, args.out_stat, "SGAT", sar_min=args.sar_min, sar_max=args.sar_max
    )
    fasta_from_SAR_dict(sars, args.out_fa)
    # stat_file_from_SAR_dict(sars,args.out_stat,sar_min=args.sar_min,sar_max=args.sar_max) # fix this whenever ready.