Rename column name from "mean" to "copy_number"

sh4nth commented 2 years ago

This will match other copy number tables and allow pd.concat to work correctly

sh4nth commented 2 years ago

I just got back from traveling and saw your comment on the other PR: https://github.com/microDM/MicFunPred/pull/5#issuecomment-1100039284

I'm happy to fix it, could you explain what you meant though?

All the existing files do not match the same format exactly 👇

==> micfunpreDefinitions/data/db/aquatic_16S_cp.txt <==
    copy_number
alpha_proteobacterium_SCGC_AAA536-G10_(unscreened)  0
alpha_proteobacterium_SCGC_AAA536-K22_(unscreened)  1

==> micfunpreDefinitions/data/db/human_16S_cp.txt <==
    copy_number
candidate division SR1 bacterium taxon 345 1OR1 (unscreened)    2
Jonquetella anthropi ADV 126, DSM 22815 3

==> micfunpreDefinitions/data/db/mammals_16S_cp.txt <==
    copy_number
Actinopolymorpha alba DSM 45243 2
Allobaculum stercoricanis DSM 13633 7

==> micfunpreDefinitions/data/db/plants_16S_cp.txt <==
    copy_number
Actinopolymorpha_alba_DSM_45243 2
Saccharibacter_floricola_DSM_15669  3

==> micfunpreDefinitions/data/db/rrnDB_16S_cp.tsv <==
name    copy_number
Komagataeibacter europaeus  4.50
Komagataeibacter xylinus    4.60

sh4nth commented 2 years ago

Ah! I see you fixed this upstream already in https://github.com/microDM/MicFunPred/commit/a64fa02700ad2103f401752571fa177939592f95

Thanks!

microDM / MicFunPred

Rename column name from "mean" to "copy_number" #7