GI numbers have been deprecated from NCBI database

chiulab / surpi

SURPI

chiulab.ucsf.edu/surpi

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GI numbers have been deprecated from NCBI database #26

Open raeece opened 8 years ago

raeece commented 8 years ago

GI numbers have been deprecated from NCBI nt/nr database since september 2016. Please see https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/ SURPI has to incorporate this change in several places of the code (eg., compare_sam.py) that relies on GI numbers to lookup for taxonomy.

ropolomx commented 7 years ago

Does anyone happen to know if someone has worked on this issue at all? I looked at the repos of people who have forked this repo but I did not see commits that addressed this. Maybe I missed this, but I would greatly appreciate if someone knows more about addressing the lack of GI numbers. Thanks!

mushalallam commented 7 years ago

Hi Did someone manage to solve this issue? Thanks