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broadinstitute / adapt

A package for designing activity-informed nucleic acid diagnostics for viruses.
MIT License
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Fix --use-fasta #64

Open priyappillai opened 2 years ago

priyappillai commented 2 years ago

--use-fasta no longer works due to automatic reference sequence finding. Example of error:

  File ".../adapt/adapt/prepare/prepare_alignment.py", line 310, in prepare_for
    for ref_acc in added_ref_accs_to_fetch:
UnboundLocalError: local variable 'added_ref_accs_to_fetch' referenced before assignment
haydenm commented 2 years ago

design.py should also be more clear in its help messages about when --use-fasta should be used versus an input type of fasta.