|
0
|
1 #!/usr/bin/env python
|
|
|
2 import sys
|
|
|
3 import argparse
|
|
|
4 from Bio import SeqIO
|
|
|
5 from Bio.Seq import Seq
|
|
|
6 from CPT_GFFParser import gffParse, gffWrite
|
|
|
7
|
|
|
8 if __name__ == "__main__":
|
|
|
9 parser = argparse.ArgumentParser(
|
|
|
10 description="Sample script to add an attribute to a feature via web services"
|
|
|
11 )
|
|
|
12 parser.add_argument("data", type=argparse.FileType("r"), help="GFF3 File")
|
|
|
13 parser.add_argument(
|
|
|
14 "--gff",
|
|
|
15 type=argparse.FileType("w"),
|
|
|
16 help="Output Annotations",
|
|
|
17 default="data.gff3",
|
|
|
18 )
|
|
|
19 parser.add_argument(
|
|
|
20 "--fasta",
|
|
|
21 type=argparse.FileType("w"),
|
|
|
22 help="Output Sequence",
|
|
|
23 default="data.fa",
|
|
|
24 )
|
|
|
25 args = parser.parse_args()
|
|
|
26
|
|
|
27 for record in gffParse(args.data):
|
|
|
28 gffWrite([record], args.gff)
|
|
|
29 record.description = ""
|
|
|
30
|
|
|
31 if isinstance(record.seq, str):
|
|
|
32 record.seq = Seq(record.seq)
|
|
|
33
|
|
|
34 SeqIO.write([record], args.fasta, "fasta")
|
|
|
35 sys.exit()
|
