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takaram / kofam_scan

CLI tool to annotate genes with KOfam
https://www.genome.jp/tools/kofamkoala/
MIT License
66 stars 11 forks source link

How to deal hmm files without a threshold & F-measure info #6

Closed lijie04 closed 4 years ago

lijie04 commented 4 years ago

Hi,

How does kofam_scan deal with hmm file that without "threshold score_type profile_type F-measure" these 4 columns information in file "ko_list", it seems to me that there will never be a valid hit of those hmms.

Thank you, Jie

lijie04 commented 4 years ago

And seems due to the situation like this, sequences are hitting other hmms positively and return those (lack important info) as negative hit.

takaram commented 4 years ago

As you noticed, you will not see KOs without thresolds as a "valid" hit. It is a weak point of this tool :(

lijie04 commented 4 years ago

Ye I see, thanks anyway