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biocore / tcga

Microbial analysis in TCGA data
BSD 3-Clause "New" or "Revised" License
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Biom t #2

Closed ekopylova closed 8 years ago

ekopylova commented 8 years ago

Script to convert Kraken output to BIOM Table.

ekopylova commented 8 years ago

@wasade could you take a look again :)?

@jkanbar this script will generate a BIOM table using results from Kraken translate command (as long as the sequences have QIIME labels).

wasade commented 8 years ago

A few minor comments. This seems okay. The use of a DataFrame works, but it likely has more overhead than indexing into a np.array or scipy.sparse.spmatrix. However, I don't think that should block here

ekopylova commented 8 years ago

@wasade @jkanbar comments have been fixed, could you merge if everything looks ok?