diff get_orfs_or_cdss.py @ 4:f97bc7f587a1 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_orfs_or_cdss.py	Mon Jun 05 02:43:41 2023 +0000
@@ -0,0 +1,92 @@
+#!/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)