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biocore / oecophylla

shotgun pipeline
MIT License
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Improved SHOGUN rule #89

Closed qiyunzhu closed 7 years ago

qiyunzhu commented 7 years ago

Now it generates the correct per-sample per-rank profiles in a format that is consistent with that of Kraken. Note that the output BIOM files contain actual lineage strings rather than TaxIDs. We still need to explore / ask Ben / Gabe to figure out how to convert lineage into TaxID.

qiyunzhu commented 7 years ago

@sjanssen2 @tanaes

wasade commented 7 years ago

Pycogent has its well,which I think ete derived from. We need to get it ported to skbio still

On Sep 22, 2017 13:56, "Jon Sanders" notifications@github.com wrote:

@tanaes commented on this pull request.

In oecophylla/taxonomy/tests/data/shogun/combined.phylum.tsv https://github.com/biocore/oecophylla/pull/89#discussion_r140595028:

@@ -0,0 +1,28 @@

  • sampleA sampleB +kArchaea;pCrenarchaeota 1.0 0.0

Note also the NCBITax functionality in ete3... it's pretty handy for these situations sometimes.

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