annotate get_orfs_or_cdss.py @ 6:f56389d8abda draft default tip

planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc

#!/usr/bin/env python
import argparse
import logging
from cpt import OrfFinder

logging.basicConfig()
log = logging.getLogger()


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Get open reading frames")
    parser.add_argument("fasta_file", type=argparse.FileType("r"), help="Fasta file")

    parser.add_argument(
        "-f",
        "--format",
        dest="seq_format",
        default="fasta",
        help="Sequence format (e.g. fasta, fastq, sff)",
    )
    parser.add_argument(
        "--table", dest="table", default=1, help="NCBI Translation table", type=int
    )
    parser.add_argument(
        "-t",
        "--ftype",
        dest="ftype",
        choices=("CDS", "ORF"),
        default="ORF",
        help="Find ORF or CDSs",
    )
    parser.add_argument(
        "-e",
        "--ends",
        dest="ends",
        choices=("open", "closed"),
        default="closed",
        help="Open or closed. Closed ensures start/stop codons are present",
    )
    parser.add_argument(
        "-m",
        "--mode",
        dest="mode",
        choices=("all", "top", "one"),
        default="all",
        help="Output all ORFs/CDSs from sequence, all ORFs/CDSs "
        "with max length, or first with maximum length",
    )
    parser.add_argument(
        "--min_len", dest="min_len", default=10, help="Minimum ORF/CDS length", type=int
    )
    parser.add_argument(
        "--strand",
        dest="strand",
        choices=("both", "forward", "reverse"),
        default="both",
        help="select strand",
    )

    parser.add_argument(
        "--on",
        dest="out_nuc",
        type=argparse.FileType("w"),
        default="out.fna",
        help="Output nucleotide sequences",
    )
    parser.add_argument(
        "--op",
        dest="out_prot",
        type=argparse.FileType("w"),
        default="out.fa",
        help="Output protein sequences",
    )
    parser.add_argument(
        "--ob",
        dest="out_bed",
        type=argparse.FileType("w"),
        default="out.bed",
        help="Output BED file",
    )
    parser.add_argument(
        "--og",
        dest="out_gff3",
        type=argparse.FileType("w"),
        default="out.gff3",
        help="Output GFF3 file",
    )
    parser.add_argument("-v", action="version", version="0.3.0")
    args = parser.parse_args()

    of = OrfFinder(args.table, args.ftype, args.ends, args.min_len, args.strand)
    of.locate(args.fasta_file, args.out_nuc, args.out_prot, args.out_bed, args.out_gff3)