Problem with revcomp() in psl_to_sequence.py

BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA

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Problem with revcomp() in psl_to_sequence.py #187

Closed bmm514 closed 2 years ago

bmm514 commented 2 years ago

Reverse complementing of the sequence is not working if the genome fasta is in lowercase. Would be useful to add in line to make sure sequence is in upper case. Could be add:

seq = seq.upper()

between line 42 and 43 in psl_to_sequence.py

lvclark commented 2 years ago

The honeybee genome Amel_HAv3.1 is a random mishmash of uppercase and lowercase letters. I just realized six months after the fact that my whole analysis is borked because all the transcript sequences generated by flair from the bottom strand of the genome are a mix of the correct sequence and its complement.

Jeltje commented 2 years ago

Thanks! This was fixed in a commit in October 2021 and is part of release 1.5.1 (which is a pre-release, we hope to do another one within a few weeks). Please reopen this ticket if you have any more issues