In line 196 of FormatAnnotation_external.py, I had to change it to
if line[2] == "gene" or line[2] == "pseudogene":
Some genes were labeled as pseudogene instead of gene and it was affecting all downstream analysis.
I suggest updating the code to something like this to support gff3 files with pseudogenes.
In line 196 of
FormatAnnotation_external.py, I had to change it toif line[2] == "gene" or line[2] == "pseudogene":Some genes were labeled as pseudogene instead of gene and it was affecting all downstream analysis. I suggest updating the code to something like this to support gff3 files with pseudogenes.