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change lca subcommands to use tax taxonomy code/handling #2198

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ctb opened this issue Aug 12, 2022 · 2 comments
Open

change lca subcommands to use tax taxonomy code/handling #2198

ctb opened this issue Aug 12, 2022 · 2 comments
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5.0 issues to address for a 5.0 release
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@ctb
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ctb commented Aug 12, 2022

The CSV parsing code in src/sourmash/lca/command_index.py is just terribly complicated and parts of it (--no-headers, for example) are not even tested.

Given the ongoing maintenance and expansion of tax taxonomy handling code, we should switch to using it (mildly ironic, since some of the tax code was based on the LCA code, I think?)

ref simplifying the way we handle identifiers, #1962

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ctb commented Aug 13, 2022

this would also support gzip input... and maybe we can change it up to support 'default' taxonomy names... ref #2195 (comment) and #2012

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ctb commented Nov 14, 2022

this would also support gzip input... and maybe we can change it up to support 'default' taxonomy names...

now in #2216

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