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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

Taxonkit list tabular output #51

Closed mweberr closed 2 years ago

mweberr commented 2 years ago

Hi, I would like to generate a tab separated output for further processing: The following output contains only spaces which makes it difficult to separate columns.

taxonkit list --ids 2157 -n -r --indent "" > archae_tree.txt

Is there an option like sep = "\t" ?

Best, Michael

shenwei356 commented 2 years ago

Pipe to taxonkit lineage, see example 5. https://bioinf.shenwei.me/taxonkit/usage/#lineage

taxonkit list --ids 2157 --indent ""  \
     | taxonkit lineage -r -n -L
mweberr commented 2 years ago

Works! Perfect, thank you