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annotate biopython_parsing.py @ 2:373c8bca8a82 draft default tip

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:57:09 +0000
parents 112751823323
children
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1 #!/usr/bin/env python
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2 # Biopython parsing module. Uses in conjunction with the sar_finder script, and potential future scripts down the line.
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4 from Bio import SeqIO
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7 class FASTA_parser:
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8 """Parses multi fasta file, and zips together header with sequence"""
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10 def __init__(self, fa):
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11 self.fa = fa
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13 def multifasta_dict(self):
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14 """parses the input multi fasta, and puts results into dictionary"""
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16 return SeqIO.to_dict(SeqIO.parse(self.fa, "fasta"))
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19 if __name__ == "__main__":
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20 fa_file = "test-data/mu-proteins.fa"
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21 d = FASTA_parser(fa_file).multifasta_dict()
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22 print(d)
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23 for k, v in d.items():
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24 print(v.description)