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annotate gff3_splitgff.py @ 3:8bd03ba8510a draft

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planemo upload commit edc74553919d09dcbe27fcadf144612c1ad3a2a2
author cpt
date Fri, 28 Apr 2023 01:35:25 +0000
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1 #!/usr/bin/env python
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2 import sys
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3 import argparse
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4 from Bio import SeqIO
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5 from Bio.Seq import Seq
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6 from CPT_GFFParser import gffParse, gffWrite
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8 if __name__ == "__main__":
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9 parser = argparse.ArgumentParser(
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10 description="Sample script to add an attribute to a feature via web services"
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11 )
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12 parser.add_argument("data", type=argparse.FileType("r"), help="GFF3 File")
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13 parser.add_argument(
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14 "--gff",
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15 type=argparse.FileType("w"),
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16 help="Output Annotations",
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17 default="data.gff3",
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18 )
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19 parser.add_argument(
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20 "--fasta",
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21 type=argparse.FileType("w"),
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22 help="Output Sequence",
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23 default="data.fa",
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24 )
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25 args = parser.parse_args()
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26
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27 for record in gffParse(args.data):
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28 gffWrite([record], args.gff)
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29 record.description = ""
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30
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31 if isinstance(record.seq, str):
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32 record.seq = Seq(record.seq)
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34 SeqIO.write([record], args.fasta, "fasta")
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35 sys.exit()