|
0
|
1 #!/usr/bin/env python
|
|
|
2 import argparse
|
|
|
3 import logging
|
|
|
4 from cpt import OrfFinder
|
|
|
5
|
|
|
6 logging.basicConfig()
|
|
|
7 log = logging.getLogger()
|
|
|
8
|
|
|
9
|
|
|
10 if __name__ == "__main__":
|
|
|
11 parser = argparse.ArgumentParser(description="Get open reading frames")
|
|
|
12 parser.add_argument("fasta_file", type=argparse.FileType("r"), help="Fasta file")
|
|
|
13
|
|
|
14 parser.add_argument(
|
|
|
15 "-f",
|
|
|
16 "--format",
|
|
|
17 dest="seq_format",
|
|
|
18 default="fasta",
|
|
|
19 help="Sequence format (e.g. fasta, fastq, sff)",
|
|
|
20 )
|
|
|
21 parser.add_argument(
|
|
|
22 "--table", dest="table", default=1, help="NCBI Translation table", type=int
|
|
|
23 )
|
|
|
24 parser.add_argument(
|
|
|
25 "-t",
|
|
|
26 "--ftype",
|
|
|
27 dest="ftype",
|
|
|
28 choices=("CDS", "ORF"),
|
|
|
29 default="ORF",
|
|
|
30 help="Find ORF or CDSs",
|
|
|
31 )
|
|
|
32 parser.add_argument(
|
|
|
33 "-e",
|
|
|
34 "--ends",
|
|
|
35 dest="ends",
|
|
|
36 choices=("open", "closed"),
|
|
|
37 default="closed",
|
|
|
38 help="Open or closed. Closed ensures start/stop codons are present",
|
|
|
39 )
|
|
|
40 parser.add_argument(
|
|
|
41 "-m",
|
|
|
42 "--mode",
|
|
|
43 dest="mode",
|
|
|
44 choices=("all", "top", "one"),
|
|
|
45 default="all",
|
|
|
46 help="Output all ORFs/CDSs from sequence, all ORFs/CDSs "
|
|
|
47 "with max length, or first with maximum length",
|
|
|
48 )
|
|
|
49 parser.add_argument(
|
|
|
50 "--min_len", dest="min_len", default=10, help="Minimum ORF/CDS length", type=int
|
|
|
51 )
|
|
|
52 parser.add_argument(
|
|
|
53 "--strand",
|
|
|
54 dest="strand",
|
|
|
55 choices=("both", "forward", "reverse"),
|
|
|
56 default="both",
|
|
|
57 help="select strand",
|
|
|
58 )
|
|
|
59
|
|
|
60 parser.add_argument(
|
|
|
61 "--on",
|
|
|
62 dest="out_nuc",
|
|
|
63 type=argparse.FileType("w"),
|
|
|
64 default="out.fna",
|
|
|
65 help="Output nucleotide sequences",
|
|
|
66 )
|
|
|
67 parser.add_argument(
|
|
|
68 "--op",
|
|
|
69 dest="out_prot",
|
|
|
70 type=argparse.FileType("w"),
|
|
|
71 default="out.fa",
|
|
|
72 help="Output protein sequences",
|
|
|
73 )
|
|
|
74 parser.add_argument(
|
|
|
75 "--ob",
|
|
|
76 dest="out_bed",
|
|
|
77 type=argparse.FileType("w"),
|
|
|
78 default="out.bed",
|
|
|
79 help="Output BED file",
|
|
|
80 )
|
|
|
81 parser.add_argument(
|
|
|
82 "--og",
|
|
|
83 dest="out_gff3",
|
|
|
84 type=argparse.FileType("w"),
|
|
|
85 default="out.gff3",
|
|
|
86 help="Output GFF3 file",
|
|
|
87 )
|
|
|
88 parser.add_argument("-v", action="version", version="0.3.0")
|
|
|
89 args = parser.parse_args()
|
|
|
90
|
|
|
91 of = OrfFinder(args.table, args.ftype, args.ends, args.min_len, args.strand)
|
|
|
92 of.locate(args.fasta_file, args.out_nuc, args.out_prot, args.out_bed, args.out_gff3)
|
