Feature/reference alleles #14
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…and fetch cluster allele representative
luissian
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saramonzon
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Feb 13, 2024
| @@ -26,6 +26,6 @@ jobs: | |||
| run: | | |||
| source $CONDA/etc/profile.d/conda.sh | |||
| conda activate taranis_env | |||
| poetry install | |||
| python -m pip install . | |||
| taranis analyze-schema -i test/MLST_listeria -o analyze_schema_test --cpus 1 --output-allele-annot --remove-no-cds --remove-duplicated --remove-subset | |||
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please add the test for the reference_alleles functionality
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I want to finish coding first, as I would like to start using pytest for testing
saramonzon
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Feb 27, 2024
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Implementation of this feature is done by creating 2 additional classes: for getting the candidate alleles
On this PR , reference alleles are selected by choosing an allele for each cluster. The cluster is done using Leigde algorithm that get as input the distance matrix created by mash program. Resolution parameter is used for Leigde algorithm to group neighborhood alleles. The resolution default or user defined value is increased by 0.025 if exists any cluster that the list of the cluster are not the same as got by blast.
Generated files are: