Gencode transcript biotype

Open ed-lau opened this issue 5 years ago • 1 comments

Hello again,

Using pip uninstall I removed the python 1.78 following which I downloaded biopython 1.77 from the source page and installed it using python setup.py install method. The installation returned no error.

Upon execution of jcast, it returned the following error:

pandas.core.computation.ops.UndefinedVariableError: name 'transcript_biotype' is not defined

Is this an error related to biopython version or is there something wrong in my command line as given below:

python -m jcast /home/jcast/diff_col/ /home/genome/gencode.v35.annotation.gtf /home/genome/GRCh38.primary_assembly.genome.fa -o /home/jcast/output/diff_col/

thanks!

Originally posted by @mranjan1 in https://github.com/ed-lau/jcast/issues/7#issuecomment-723237130

Nov 06 '20 20:11 ed-lau

Ok, with the last change, I see that jcast has advanced to the step where it's reading the rMATS output file. It started with processing MXE junctions. This has definitely resolved the UndefinedVariableError. I'm going to let it run and see how long it takes.

Thank you so much Dr. Lau.

Nov 06 '20 21:11 mranjan1