with absolute abundance

Thank you very much for the script- this was really helpful!

I would like to also add the clade_ids / tax_ids to the merged table (in the single profiles they are present, but in the merged table not anymore). Do you know, how I can do this? I tried the script added here and it gives me around 1/3 of the IDs but most rows stay empty…

Best and thank you again


6d_merge_metaphlan_tables_V4absID.txt (3.5 KB)

Could you try to use a modified script from my comment above, and modify line 34 as:
iIn = pd.read_csv(f, sep='\t', skiprows=len(headers), names=names, usecols=[0,1,4] if not gtdb else range(4), index_col=[0,1])

This should be enough to do the job.


1 Like

Thank you very very much for the fast response! I will let you know :slight_smile: