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Allow query cluster assignment without taxonomy #33

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Robaina opened this issue Jan 24, 2022 · 1 comment · Fixed by #34
Closed

Allow query cluster assignment without taxonomy #33

Robaina opened this issue Jan 24, 2022 · 1 comment · Fixed by #34
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bug Something isn't working enhancement New feature or request important Preferably work on this

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@Robaina
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Robaina commented Jan 24, 2022

So far, labelplacements.py only works for MARdb sequences with valid MMP identifiers (so a taxonomic path can be retrieved from the GTDB database). However, this method prevents cluster assignment to query sequences when reference sequences don't come from MARdb.

This issue will modify:

https://github.com/Robaina/TRAITS/blob/7ca208a0bb593dea9ebec5c20a99877e7d60ad3f/code/phyloplacement/placement.py#L371-L389

to allow taxonomy-free cluster assignment.

To this end, we can create a fake taxopath only containing the cluster name (perhaps additional fields if required, it doesn't matter). Gappa examine assign should then assign clusters to placed queries as if it had a valid taxopath

@Robaina Robaina added bug Something isn't working enhancement New feature or request important Preferably work on this labels Jan 24, 2022
@Robaina Robaina self-assigned this Jan 24, 2022
Robaina added a commit that referenced this issue Jan 25, 2022
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Robaina commented Jan 25, 2022

Pull Request #34 solved this issue, clusters can now be assigned to queries independent of taxonomy

Robaina added a commit that referenced this issue Feb 22, 2023
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