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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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biom convert is not case sensitive #556

Closed wdwvt1 closed 9 years ago

wdwvt1 commented 9 years ago

biom convert -i TEST.biom -o xyz.txt --to-tsv --table-type='OTU table' and biom convert -i test.biom -o xyz.txt --to-tsv --table-type='OTU table' both work, regardless of the case of of TEST.biom.

This seems like unexpected behavior (and I have looked through the documentation but can't find a reference to this being expected). I can't see many situations where it would be a problem, but perhaps with the output of split_otu_table.py it could be a problem if someone has metadata that is differentiated by character case alone.

wasade commented 9 years ago

Sure that isn't your filesystem? On Oct 20, 2014 8:56 PM, "Will Van Treuren" notifications@github.com wrote:

biom convert -i TEST.biom -o xyz.txt --to-tsv --table-type='OTU table' and biom convert -i test.biom -o xyz.txt --to-tsv --table-type='OTU table' both work, regardless of the case of of TEST.biom.

This seems like unexpected behavior (and I have looked through the documentation but can't find a reference to this being expected). I can't see many situations where it would be a problem, but perhaps with the output of split_otu_table.py it could be a problem if someone has metadata that is differentiated by character case alone.

— Reply to this email directly or view it on GitHub https://github.com/biocore/biom-format/issues/556.

wdwvt1 commented 9 years ago

well now I feel sheepish...

wasade commented 9 years ago

:) glad you got it sorted out On Oct 20, 2014 9:11 PM, "Will Van Treuren" notifications@github.com wrote:

Closed #556 https://github.com/biocore/biom-format/issues/556.

— Reply to this email directly or view it on GitHub https://github.com/biocore/biom-format/issues/556#event-181291731.