QAPA fasta ERRO

[wqy399]

Hi, when I use QAPA to extract sequences from mm10.fa with the following command: qapa fasta -f mm10_ucsc.fa output_utrs.bed output_sequences.fa, I got this error:TypeError: expected str, bytes or os.PathLike object, not FileInput.

Could you please help me to figure out what's wrong with it.
Here is part of the bed file.

Would you please help me to figure out what's wrong with that ?

[wqy399]

Python version is 3.7, bedtools version is 2.25.0

[quaidmorris]

Is mm10_ucsc.fa uncompressed and in the directory that you are calling qapa from?

[wqy399]

Thanks for your reply.
Yes. I am sure the fasta file located correctly in the same directory. And I guess this ERRO has something with the python versions or configs or something like that. This problem really confuses me for days and my lab-mates can not figure out as well.

Thats all the files in the directory. I got the output_sequences.fa but it is empty.
A lot thanks for your help!

[kcha]

Can you try downgrading Biopython (maybe 1.76?). The error seems to be something related to that package. Maybe there was a breaking change, but I'm not sure.

[wqy399]

Wow! It worked well after I degraded the Biopython to version 1.76.
Thanks a lot!!!!!!

[kcha]

Thanks for catching this. I will make some changes to address this issue when I get the chance.