Hi,
Despite looking into several topics on the qiime forum, e.g. Biom add metadata problem i did not manage to solve this.
I tried to add the taxonomy information to the biom file. I changed the header in the taxonomy file to #OTUID but i do not see my taxonomy information when i open the .txt file converted from the .biom file.
I tried this:
qiime tools export --input-path ./tableWesternDietSert.qza --output-path ./
qiime tools export --input-path ./taxonomy_rep-seqs.qza --output-path ./
biom add-metadata -i feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp taxonomy.tsv --observation-header OTUID,Taxon,Confidence
biom convert -i table-with-taxonomy.biom -o table.from_biom_with_taxonomy.txt --to-tsv
In the above topic i saw you need to add –header-key taxonomy so i tried this:
biom convert -i table-with-taxonomy.biom -o table.from_biom_with_taxonomy.txt --to-tsv --header-key taxonomy
but when i do this i get a phyton related error message:
Traceback (most recent call last):
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/bin/biom”, line 11, in
sys.exit(cli())
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/click/core.py”, line 76n call
return self.main(*args, **kwargs)
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/click/core.py”, line 71n main
rv = self.invoke(ctx)
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/click/core.py”, line 11in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/click/core.py”, line 95n invoke
return ctx.invoke(self.callback, **ctx.params)
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/click/core.py”, line 55n invoke
return callback(*args, **kwargs)
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/biom/cli/table_converte”, line 129, in convert
table_type, process_obs_metadata, tsv_metadata_formatter)
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/biom/cli/table_converte”, line 185, in _convert
metadata_formatter=obs_md_fmt_f)
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/biom/table.py”, line 48in to_tsv
observation_column_name)
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/biom/table.py”, line 16in delimited_self
md_out = metadata_formatter(md.get(header_key, None))
File “/sw/arch/RedHatEnterpriseServer7/EB_production/2019/software/QIIME2/2019.4/lib/python3.6/site-packages/biom/cli/table_converte”, line 36, in
‘sc_separated’: lambda x: '; '.join(x),
TypeError: can only join an iterable
Do you have advice on how to add the taxonomic information?
Thank you.
Bests Mirjam