How to remove taxonomy in biom files, and save it as qza (python) ?

[Wang_cs001632]

We want to remove 100 OTU ids from a 10000 OTU table. Could you kindly suggest how to directly manipulate and delete OTUs from a biom file, then save it as qza (python).
Thank you for your help!
Code example:
def read_filter(val, id_, md):
print(id_)
return id_ in toBeFiltered_idx
table2 = table.copy().filter(read_filter, axis='observation')

[timanix (Timur Yergaliyev)]

Hi!
You can import your biom to qiime first:

qiime tools import \
  --input-path feature-table.biom \
  --type 'FeatureTable[Frequency]' \
  --input-format BIOMV210Format \
  --output-path table.qza

And then remove undesired OTUs using this plugin.

Another option is to convert your biom into tsv file, manipulate it, and convert back to a biom file and then import it to qiime:

convert .biom to .tsv

biom convert -i feature-table.biom -o feature-table.tsv --to-tsv 
biom convert -i feature-table.tsv -o feature-table.biom --table-type="OTU table" --to-hdf5

All commands above can be executed in the terminal or in the Jupyter (put "!" before terminal command)