TypeError: '<' not supported between instances of 'NoneType' and 'int' when running predict module about ribotish HOT 5 CLOSED

https://github.com/zhpn1024/ribotish/commit/ed3d80d5aed2e504c2eb120f8b6e51b05db14acf

from ribotish.

Thank you for reporting the bug. Let me see how to deal with it.

from ribotish.

The problem is that the 'start_codon' line is missing, and the code calculate start codon position with stop codon, resulting in frame shift error. The t.cds_start(cdna=True) should be 0 instead of 2, and t.cds_stop(cdna=True) should be 1335.
Deleting the second stop_codon line should be fine.
I have find a way to fix the bug.

from ribotish.

Thanks for the timely response.

By the way, I am not sure whether self.cds_start have similar problems when "start_codon" lines are present in gtf. It is possible that a start codon might be distributed over two exons in rare cases, which might also lead to incorrect results in cds_start() class mehtod.

from ribotish.

You are right. The split of start codon should also be considered.

from ribotish.