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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 import logging
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5 from Bio import SeqIO
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6
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7 logging.basicConfig(level=logging.INFO)
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8 log = logging.getLogger()
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9
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10
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11 def drop_id(fasta_file=None):
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12 for rec in SeqIO.parse(fasta_file, "fasta"):
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13 rec.description = ""
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14 ind = str(rec.seq).find("##")
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15 if (
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16 ind != -1
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17 ): # This method causes mid-file comments (such as from Apollo sequences) to be appended to the end of the previous sequence
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18 rec.seq = rec.seq[0:ind]
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19 yield rec
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20
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21
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22 if __name__ == "__main__":
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23 parser = argparse.ArgumentParser(description="Identify shine-dalgarno sequences")
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24 parser.add_argument("fasta_file", type=argparse.FileType("r"), help="Genbank file")
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25
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26 args = parser.parse_args()
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27 for rec in drop_id(**vars(args)):
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28 SeqIO.write([rec], sys.stdout, "fasta")
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