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immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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EstimateError.py pandas bug. #53

Closed ssnn-airr closed 7 years ago

ssnn-airr commented 7 years ago

Original report by Anonymous.

EstimateError.py nuc_df pandas bug. Unfortunately I didn't record the output. These lines are involved. 

lines 208 to 213:
        #nuc_pairs = list(permutations(['A', 'C', 'G', 'T'], 2))
        #nuc_index = pd.MultiIndex.from_tuples(nuc_pairs, names=['obs', 'ref'])
        nuc_index = pd.MultiIndex(levels=[[], []], labels=[[], []], names=['obs', 'ref'])
        nuc_df = pd.DataFrame(None, index=nuc_index,
                              columns=['mismatch', 'q_sum', 'total'],
                              dtype=float)
ssnn-airr commented 7 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

I fixed a division by zero error when there were no mismatches in 09922c7. Kinda hard to tell if it's the same issue without input, output and trace.

If this isn't the same issue, reopen when it appears again.