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docs: fix documentation for newreference.py to reflect --gene behavior #60

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Jun 5, 2024
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docs: fix documentation for newreference.py to reflect --gene behavior #60

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4 changes: 2 additions & 2 deletions scripts/newreference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,8 @@ def new_reference(referencefile, outgenbank, outfasta, gene):
startofgene = int(list(feature.location)[0])
endofgene = int(list(feature.location)[-1])+1

# If user provides a --gene 'some name' is not found, print a warning and use the entire genome.
# Otherwise do not print a warning.
# If user provides a --gene 'some name' that is not found, error out as this may indicate that
# the gene name is misspelled or the user may be using the wrong GenBank file.
if(gene is not None and startofgene is None and endofgene is None):
print(f"ERROR: No '{gene}' was found under 'gene' or 'CDS' features in the GenBank file.", file=sys.stderr)
sys.exit(1)
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