Harrison Deng
42d73270b3
Finished program with additional functions such as: * Custom search string * Custom search location
66 lines
1.5 KiB
Python
Executable File
66 lines
1.5 KiB
Python
Executable File
#!/usr/bin/env python3
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import os
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from Bio import SeqIO
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import argparse
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def main(args):
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kept_records = []
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for s_record in SeqIO.parse(args.input, "fasta"):
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if args.property != "all" and not (
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args.contains in getattr(s_record, args.property)
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):
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kept_records.append(s_record)
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elif args.property == "all" and not (
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args.contains in s_record.id
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and args.contains in s_record.name
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and args.contains in s_record.description):
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kept_records.append(s_record)
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SeqIO.write(
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kept_records,
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os.path.abspath(args.output),
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"fasta"
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)
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if __name__ == "__main__":
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argparser = argparse.ArgumentParser(
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"Removes sequences where id contains certain string.")
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argparser.add_argument(
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"input",
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type=str,
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metavar="i",
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help="The input fasta file."
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)
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argparser.add_argument(
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"output",
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type=str,
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metavar="o",
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help="The output file path."
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)
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argparser.add_argument(
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"-c",
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"--contains",
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type=str,
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default=None,
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required=False,
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help="The string to search for."
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)
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argparser.add_argument(
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"-p",
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"--property",
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type=str,
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default="all",
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required=False,
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help="""
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The part of the fasta file to look through. Valid options are: id,
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name, description, or all.
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"""
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)
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main(argparser.parse_args())
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