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noriakis / ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics
https://noriakis.github.io/software/ggkegg
MIT License
214 stars 16 forks source link

Using convert_id() without REST_API #38

Open w2felix opened 2 months ago

w2felix commented 2 months ago

can I use local files downloaded from the KEGG ftp to run convert_id functions? I would like to let the package run on a machine without internet. Best wishes Felix

noriakis commented 2 months ago

Thank you always for your suggestion. This is indeed an important feature and I will definitely implement one for specifying the converting table without accessing REST API.

noriakis commented 2 months ago

Hi, in 88a401b, convert_id now has following arguments:

file: file for converting IDs query_column: query column number convert_column: convert column number pref: prefix to be added (optional) to the query column

I think most of the cases can be covered including files from downloaded KEGG data, but let me hear your thought!

w2felix commented 2 months ago

sounds reasonable, will test it later