I need help understanding precisely how
qiime feature-table rename-ids works, especially its metadata file and column parameters. Or maybe I'm using the wrong tool, and would welcome advice on a better approach. I've searched already (Merging Error Table and RepSeq was useful but not directly solving if I read it right); I've read the glossary; I'm running qiime2-2021.2 through conda.
My feature tables are full of ids that are 36-character-long alphanumeric codes (e.g., "cc7f7cd6d961f50ae6d57a7513b2818e") and I aim to replace these codes with their more intelligible taxonomy labels (e.g., "d__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Gammaproteobacteria_Incertae_Sedis; f__Unknown_Family; g__Acidibacter; s__uncultured_eubacterium"). Tried writing my own script to replace the 36-character codes with just the associated "s__uncultured_eubacterium" (or whatever the most specific taxon is), but such a label is not unique and cannot serve as metadata ID. Tweaked the script so I appended the long code to the useful label, and edited so it's all keemei-approved (36 approvable characters), resulting in the above example being something like "s-uncultured-eubacterium-cc7f7cd6d9". This replacement for a whole feature table truly seems impossible/impractical manually, but should be easy with cli powers ... I just need superior expertise.
I have an unintelligible feature table. I have a metadata table consisting of one column, labeled 'ID'. I run
qiime feature-table rename-ids --i-table deblur_output/deblur_table_final.qza --m-metadata-file meta_renaming --m-metadata-column 'ID' --o-renamed-table renamed_table
and find that my result is
(1/1) Invalid value for '--m-metadata-file': There was an issue with retrieving column 'ID' from the metadata.
I find this counter-intuitive to trouble-shoot. It also doesn't work without quotation marks around 'ID' in the metadata column parameter.
Following some thinking from Merging Error Table and RepSeq, I also tried
qiime metadata tabulate --m-input-file deblur_output/deblur_table_final.qza --m-input-file meta_renaming --o-visualization merged.qzv --verbose
to see how it worked out and got
`Traceback (most recent call last):
File "/home/cory/anaconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/click/option.py", line 182, in type_cast_value
File "/home/cory/anaconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/metadata/metadata.py", line 694, in merge
"Cannot merge because there are no IDs shared across metadata "
ValueError: Cannot merge because there are no IDs shared across metadata objects.
There was an issue with merging QIIME 2 Metadata:
Cannot merge because there are no IDs shared across metadata objects.
See above for debug info.`
This error is clear, but making the IDs be the same is precisely what I'm trying to do here. (This also doesn't work with a transposed table, just in case that mattered.)
I have attached all files referred to: my feature table (deblur_table_final.qza), the taxonomy.tsv table linking codes to taxonomy (taxonomy.tsv), my (keemei-approved) metadata file (meta_renaming.txt), my representative sequences (rep_seqs_final.qza), and even the horrifying script I kludged up to grab more-useful labels from taxonomy.tsv (renaming.txt).
deblur_table_final.qza (150.5 KB)
taxonomy.tsv (2.4 MB)
meta_renaming.txt (596.5 KB)
rep_seqs_final.qza (151.0 KB)
renaming.txt (489 Bytes)
As always, I've tried to be both complete and concise. Sorry for any obvious failures. And my thanks to anyone who can help.
[Edit to move a tick mark.]