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
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Unnecessary stdin check for taxonkit filter? #36

Closed standage closed 3 years ago

standage commented 3 years ago

In TaxonKit 0.7, I get the following error.

$ taxonkit filter --list-order
23:31:23.142 [ERRO] stdin not detected

The command is checking for stdin, even when input is not used. Can fix by echoing an empty string, but that seems unnecessary.

$ echo '' | taxonkit filter --list-order | tail
species
forma specialis,pathovar,subspecies
pathogroup,serogroup
biotype,genotype,serotype
aberration,morph,varietas,variety
subaberration,submorph,subvarietas,subvariety
form,forma
subform,subforma
strain
isolate

The same is true for taxonkit filter --list-rank.


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shenwei356 commented 3 years ago

Oh, sorry, I fix this.

shenwei356 commented 3 years ago

Should I release a new version?

standage commented 3 years ago

Wow, that was fast!

Should I release a new version?

Maybe wait? I will continue updating bindings tomorrow, and I may encounter other questions.

standage commented 3 years ago

Maybe wait? I will continue updating bindings tomorrow, and I may encounter other questions.

Ok, with recent fixes in #36 and #37 I haven't found any other bugs or questions about software behavior. You're welcome to release a new version whenever it's convenient for you.

Thanks for your excellent responses!