hdallatorre commited on
Commit
2657c8e
1 Parent(s): 3550519

feat: Use python builtins instead of seqio

Browse files
nucleotide_transformer_downstream_tasks.py CHANGED
@@ -18,7 +18,25 @@ Transformer paper."""
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  from typing import List
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  import datasets
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- from Bio import SeqIO
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  # Find for instance the citation on arxiv or on the dataset repo/website
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  _CITATION = """\
@@ -131,12 +149,12 @@ class NucleotideTransformerDownstreamTasks(datasets.GeneratorBasedBuilder):
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  def _generate_examples(self, file):
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  key = 0
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  with open(file, "rt") as f:
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- fasta_sequences = SeqIO.parse(f, "fasta")
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- for record in fasta_sequences:
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  # parse descriptions in the fasta file
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- sequence, name = str(record.seq), str(record.name)
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  label = int(name.split("|")[-1])
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  # yield example
 
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  from typing import List
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  import datasets
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+
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+
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+ # This function is a basic reimplementation of SeqIO's parse method. This allows the
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+ # dataset viewer to work as it does not require an external package.
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+ def parse_fasta(fp):
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+ name, seq = None, []
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+ for line in fp:
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+ line = line.rstrip()
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+ if line.startswith(">"):
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+ if name:
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+ # Slice to remove '>'
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+ yield (name[1:], "".join(seq))
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+ name, seq = line, []
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+ else:
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+ seq.append(line)
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+ if name:
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+ # Slice to remove '>'
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+ yield (name[1:], "".join(seq))
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+
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  # Find for instance the citation on arxiv or on the dataset repo/website
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  _CITATION = """\
 
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  def _generate_examples(self, file):
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  key = 0
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  with open(file, "rt") as f:
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+ fasta_sequences = parse_fasta(f)
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+ for name, seq in fasta_sequences:
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  # parse descriptions in the fasta file
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+ sequence, name = str(seq), str(name)
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  label = int(name.split("|")[-1])
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  # yield example