Update build script for changes to NCBI ranks #69
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tibvdm
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Mar 20, 2025
| -e 's/serotype/no rank/' -e 's/clade/no rank/' \ | ||
| -e 's/isolate/no rank/' -e 's/infraclass/no rank/' \ | ||
| -e 's/parvorder/no rank/' "$TEMP_DIR/$UNIPEPT_TEMP_CONSTANT/nodes.dmp" | ||
| -e 's/parvorder/no rank/' -e 's/no_rank/domain/' "$TEMP_DIR/$UNIPEPT_TEMP_CONSTANT/nodes.dmp" |
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For clarity: Are the substitutions sequential? As in, will the last substitution not set all previous replacements to 'domain'?
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It doesn't matter, since NCBI uses no_rank (with an underscore) and we've always used no rank (with a space). I will, anyways, update the order to improve the readability here :)
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This PR updates the
build_database.shscript with support for the newdomainandrealmNCBI ranks. NCBI also changed the rank of the Viruses node tono_rank. Internally, we are mapping this back todomainto make sure that our LCA computations further downstream keep working.In order to make sure that the desktop app still works, I have also updated the static database construction action. This one now generates two static databases: 1) a copy of the current database (which still contains the superkingdom rank and is compatible with the desktop app) and 2) an up-to-date database which is labeled as v2.