Translate MetaPhlAn2 taxonomy terms back to NCBI TaxIDs

biocore / oecophylla

shotgun pipeline

MIT License

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Translate MetaPhlAn2 taxonomy terms back to NCBI TaxIDs #94

Closed qiyunzhu closed 7 years ago

qiyunzhu commented 7 years ago

Currently I have a work around that maps all MetaPhlAn2 terms from kingdom to species to NCBI TaxIDs. Strains can't be mapped because there is no "strain" level in NCBI. In some cases, taxa below species in NCBI were raised to species in MetaPhlAn2. What to do with them is an open question. Leaving them as is may cause inconsistency when comparing to other profilers. Merging them to higher level species / genus will reduce the resolution of MetaPhlAn2.

tanaes commented 7 years ago

Is this currently handled with rule in dev?

qiyunzhu commented 7 years ago

@tanaes Yes it is taken care of. We will need @sjanssen2 to generate that dictionary externally.

tanaes commented 7 years ago

resolved in #118