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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
361 stars 29 forks source link

No output for leaf nodes of the taxonomy #4

Closed ialbert closed 7 years ago

ialbert commented 7 years ago

Hello,

I am playing around with taxonkit and I got puzzled by its behavior. It looks like it will not produce output when searching for leaf nodes of the taxonomic tree. For example, this prints nothing:

taxonkit list --show-rank --ids 9913

same with lineage etc. Any time I search for a node with no children I get nothing back.

I am not sure I understand what is the rationale for this. Is this working as intended?

How would one use taxonkit to figure out that 9913 is the the taxid for Bos Taurus? le

shenwei356 commented 7 years ago

fixed in v0.2.1:

$ taxonkit list --show-rank --show-name --ids 9913
[INFO] parsing names file: /home/shenwei/.taxonkit/names.dmp
[INFO] 1593209 names parsed
[INFO] parsing nodes file: /home/shenwei/.taxonkit/nodes.dmp
[INFO] 1593209 nodes parsed
9913 [species] Bos taurus
ialbert commented 7 years ago

great, thanks!

ialbert commented 7 years ago

One more suggestion from a usability perspective. Having the tool always print debug information (sometimes even multiple times during one operation) is distracting from the task that one tries to accomplish. Sometimes it is hard to see the actual result because of this.

[INFO] parsing names file: /Users/ialbert/.taxonkit/names.dmp
[INFO] 1629550 names parsed
[INFO] parsing nodes file: /Users/ialbert/.taxonkit/nodes.dmp
[INFO] 1629550 nodes parsed
shenwei356 commented 7 years ago

ok, i'll make them as optional output tomorrow.

shenwei356 commented 7 years ago

v0.2.2

$ taxonkit list --show-rank --show-name --ids 9913
9913 [species] Bos taurus
ialbert commented 7 years ago

nice thanks!

shenwei356 commented 7 years ago

I'm so sorry, I just fixed a bug brought in v0.2.1 :( , see v0.2.3.