Merge_metaphlan_tables.py with absolute abundance

Microbial community profiling MetaPhlAn
#1

Hi all!
In case if someone will need it, here is the modified file that merges absolute abundances instead of relative abundances in metaphlan output (you should run metaphlan with ‘-t rel_ab_w_read_stats’ option).
merge_metaphlan_tables_abs.txt (3.6 KB)
Rename it as merge_metaphlan_tables_abs.py and make it executable. Usage is the same as for relative abundance merging.

6 Likes
Merge_metaphlan_tables.py with rel_ab_w_read_stats
Merged abundance table to biom format
#2

Thank you very much. I needed this!

1 Like
#3

This worked perfectly, thank you!

1 Like
#4

Thank you very much for this, Tim!

1 Like
#5

Thanks, Timyerg. This is really what I need!
May I know where should we upload this file?
I try to upload it to the files relevant to Metaphlan, but it seems that the command not been found.
Much appreciated it if you could give any suggestions,

#6

You are welcome!

  1. Download the file. Put it anywhere.
  2. Rename it to replace “.txt” extension to “.py”
  3. Make it executable (replace “path_to” with a path to file):
    chmod +x path_to/merge_metaphlan_tables_abs.py
  4. Run it as original script, but provide path_to/merge_metaphlan_tables_abs.py in a command, with a path to the script.
#7

Many thanks for your quick reply! Timyerg. It works well!

#8

It is so nice of you! truely appreciate your work!