make csv to qza

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#1

hi

I want to convert the shannon number calculated in R to qza.

I made a biom file with biom convert -i shannon_share.tsv -o new_otu_table.biom --to-hdf5.

next
qiime tools import --input-path new_otu_table.biom --input-format BIOMV100Format --output-path shannon.qza --type

–type Which one should I choose next?

Thank you.

#2

Could you try "SampleData[AlphaDiversity]"

#3

I tried, but I got an error.

Traceback (most recent call last):
File “/data/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/builtin/tools.py”, line 158, in import_data
view_type=input_format)
File “/data/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 241, in import_data
validate_level=‘max’)
File “/data/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 266, in _from_view
recorder=recorder)
File “/data/miniconda3/envs/qiime2-2020.11/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.AlphaDiversityDirectoryFormat’>

An unexpected error has occurred:

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

See above for debug info.

#4

Why did you convert it to biom? If you want a shannon.qza, as it produced in Qiime, you should use a .tsv file.
If you just want to add this metric to feature table, use 'FeatureTable[Frequency]'

#5

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