I do understand that what you call a TSV-formatted (classic) table is not considered to be a BIOM format file, but the behaviour of biom validate-table given such a file is not ideal.
I would like the validate-table help to be explicit about this:
$ biom validate-table -h
Usage: biom validate-table [OPTIONS]
Validate a BIOM-formatted file.
Test a file for adherence to the Biological Observation Matrix (BIOM) format
specification. This specification is defined at http://biom-format.org
Example usage:
Validate the contents of table.biom for adherence to the BIOM format
specification
$ biom validate-table -i table.biom
Options:
-i, --input-fp FILE The input filpath to validate against the BIOM
format specification [required]
-f, --format-version TEXT The specific format version to validate against
-h, --help Show this message and exit.
I do understand that what you call a TSV-formatted (classic) table is not considered to be a BIOM format file, but the behaviour of
biom validate-table
given such a file is not ideal.I would like the validate-table help to be explicit about this:
Example of current behaviour:
Expected behaviour:
Clear error message like "This file is not in HDF5 or JSON format" or better "This is a TSV file, not a BIOM file." (edited to fix missing pronouns)