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shenwei356 / taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
https://bioinf.shenwei.me/taxonkit
MIT License
357 stars 29 forks source link

Feature request: report specific lineage ranks #72

Closed soungalo closed 1 year ago

soungalo commented 1 year ago

When using the lineage command, it would be useful to have an option to specify which ranks should be reported, e.g.: taxonkit lineage --show-lineage-ranks --report-ranks "family,genus,species".

shenwei356 commented 1 year ago

Please use taxonkit reformat

$ echo 562 | taxonkit reformat -I 1 -f '{f},{g},{s}'
562     Enterobacteriaceae,Escherichia,Escherichia coli