workflow when importing biom table without sequences

[rajesh512 (Rajesh)]

Hi everyone, I am running QIIME2 on macOS Catalina and have a question about workflow. I am using a biom table generated using QIIME 1 and would like to perform taxonomic comparisons. I successfully imported the table to create an feature-table artifact (frequency). From what I read in the tutorials, to do this I need a sequence table also, which I don’t have. Is there a workaround for this? Thanks

[colinbrislawn (Colin J Brislawn)]

Hello Rajesh,

@rajesh512

I am using a biom table generated using QIIME 1 and would like to perform taxonomic comparisons.

Cool! Qiime 1 tables will always contain a feature abundance table, but they can include a taxonomy table inside the same file. You might be good to go!

@rajesh512

I successfully imported the table to create an feature-table artifact (frequency).

Cool!

If your Qiime 1 .biom table does have the taxonomy table build into it, we just need to figure out how to get it imported into Qiime 2.

If your Qiime 1 .biom table does not have taxonomy, then we will need to make a taxonomy table ourselves using a qiime 2 feature classifier...
... and the feature classifier needs a sequence table or sequence file (.fna or .fasta).

---

One easy way to figure out if your .biom table has taxonomy in it is to use the tail command and look for taxonomy strings. Try that!
tail -c200 otus.biom

Colin

[thermokarst]

@colinbrislawn

One easy way to figure out if your .biom table has taxonomy in it is to use the tail command and look for taxonomy strings. Try that!
tail -c200 otus.biom

This only works if the file is for the old-style BIOM 1 format, which has been replaced with the 2.1.0 format in recent years.

You can import a taxonomy-annotated biom file as both FeatureTable[Frequency] & FeatureData[Taxonomy]:

qiime tools import \
  --input-path my-file.biom \
  --output-path my-taxonomy.qza \
  --source-format BIOMV210Format \
  --type "FeatureData[Taxonomy]"

[rajesh512 (Rajesh)]

Matthew, thanks for the comment and clarification. I’m unclear when to use FeatureData versus FeatureTable for the type argument. I tried the below command and received the subsequent error. I have a table that is BIOM format 100 and it does contain taxonomy data. I assume FeatureTable is the correct type, but when I try that the imported table/artifact does not contain taxonomy data. Thanks

qiime tools import --input-path RISK_all_samples.biom --type ‘FeatureData[Taxonomy]’ --input-format BIOMV100Format --output-path feature_table_v1.qza

Traceback (most recent call last):
File “/Users/rajeshshah/miniconda3/envs/qiime2.2019-7/lib/python3.6/site-packages/q2cli/builtin/tools.py”, line 154, in import_data
view_type=input_format)
File “/Users/rajeshshah/miniconda3/envs/qiime2.2019-7/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 241, in import_data
validate_level=‘max’)
File “/Users/rajeshshah/miniconda3/envs/qiime2.2019-7/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 266, in _from_view
recorder=recorder)
File “/Users/rajeshshah/miniconda3/envs/qiime2.2019-7/lib/python3.6/site-packages/qiime2/core/transform.py”, line 59, in make_transformation
(self._view_type, other._view_type))
Exception: No transformation from <class ‘q2_types.feature_table._format.BIOMV100Format’> to <class ‘qiime2.plugin.model.directory_format.TSVTaxonomyDirectoryFormat’>

An unexpected error has occurred:

No transformation from <class ‘q2_types.feature_table._format.BIOMV100Format’> to <class ‘qiime2.plugin.model.directory_format.TSVTaxonomyDirectoryFormat’>

See above for debug info.

[thermokarst]

You will need to convert your biom table to biom 2.10 format first:

biom convert -i RISK_all_samples.biom -o hdf5_table.biom --table-type="OTU table" --to-hdf5

qiime tools import --input-path hdf5_table.biom --type ‘FeatureData[Taxonomy]’ --input-format BIOMV210Format --output-path feature_table_v1.qza

Give that a shot and let us know how it goes!

[rajesh512 (Rajesh)]

Matthew,

Thanks again for your response. I ran the below commands, was able to import the biom table with taxonomy data within it, convert it to a relative abundance table and then filter it. Then I tried to convert back to a classic table (txt) to format it for MaasLin. When I do that conversion back and ask for taxonomy data as the last column, it again is blank. I’m not sure I understand why it appears to be in the table, but then gets dropped. When I import using FeatureTable, does this import a biom table containing frequency information and the taxonomy?

The basic process I am trying to perform, is take a biom version 100 table, convert it to a relative frequency table (for MaasLin), reformat the taxonomy data for Maaslin and then run it through the Galaxy web based interface.

Thanks again for your help.

#import new hdf5 biom table to create artifact

qiime tools import --input-path hdf5_table.biom --type ‘FeatureTable[Frequency]’ --input-format BIOMV210Format --output-path hdf5_all.qza

#convert frequency table to relative abundance table
qiime feature-table relative-frequency --i-table hdf5_all.qza --o-relative-frequency-table hdf5_all_rel_ab.qza

#filter tables for controls and patients with CD
qiime feature-table filter-samples --i-table hdf5_all_rel_ab.qza --m-metadata-file RISK_metadata_no_mixed.txt --p-where “[Diagnosis]=‘CD’” --o-filtered-table CD_hdf5_rel_ab.qza

qiime feature-table filter-samples --i-table hdf5_all_rel_ab.qza --m-metadata-file RISK_metadata_no_mixed.txt --p-where “[Diagnosis]=‘non-IBD’” --o-filtered-table Ctrls_hdf5_rel_ab.qza

#convert biom table back to txt format
biom convert -i CD_hdf5_rel_ab/data/feature-table.biom -o CD_hdf5_rel_ab.txt --to-tsv --header-key taxonomy

[thermokarst]

@rajesh512

#convert biom table back to txt format
biom convert -i CD_hdf5_rel_ab/data/feature-table.biom -o CD_hdf5_rel_ab.txt --to-tsv --header-key taxonomy

Before running this step, check out this tutorial:

Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)

Creating a TSV BIOM table The following is based on a post by @gregcaporaso. $ qiime tools export table.qza --output-dir ./ $ biom convert -i feature-table.biom -o feature-table.tsv --to-tsv $ biom head -i feature-table.tsv # Constructed from biom file #OTU ID L1S105 L1S140 L1S208 L1S257 L1S281 4b5eeb300368260019c1fbc7a3c718fc 2222.0 0.0 0.0 0.0 0.0 fe30ff0f71a38a39cf1717ec2be3a2fc 5.0 0.0 0.0 0.0 0.0 d29fe3c70564fc0f69f2c03e0d1e5561 0.0 0.0 0.0 0.0 0.0 868528ca947bc57b69ffdf83e6b73bae 0.0 227…