Thanks @thermokarst
I think I still must be missing something and still have trouble moving things from python to q2 to R and back. Right now I have my feature table, tax table, and metadata as three panda's dataframes. To save the metadata and import into q2 I can use
# save to disk in python
meta_sample_update.to_csv('meta_update.csv', index=False)
# read into q2 bash - or bring in with any function that needs metadata
!qiime metadata tabulate \
--m-input-file metadata_mapping.tsv \
--o-visualization tabulated-sample-metadata.qzv
But I seem to be getting stuck with the tax and feature tables. I've tried:
# save to disk bash
!ASV_df_control_ASV_removed.save('ASV_update.qza')
returns
/usr/bin/sh: -c: line 0: syntax error near unexpected token `'ASV_update.qza''
/usr/bin/sh: -c: line 0: `ASV_df_control_ASV_removed.save('ASV_update.qza')'
and
#save to disk python
ASV_df_control_ASV_removed.save('ASV_update.qza')
returns
AttributeError: 'DataFrame' object has no attribute 'save'
Is there a save module from q2 that I need to import?
Once I have the tables saved to disk as qza files, can I import them into q2 using:
ASV_file.qza = Artifact.import_data("FeatureTable[Frequency]", feature_wide)
tax_file.qza = Artifact.import_data("TaxonomyTable")
Thank you