Inconsistence Gene IDs used in gtf_preprocess.py #6
Description
Whilst using gtf_preprocess.py to create the expandCDS.fasta file, I obtained the following error:
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/scikit-ribo/gtf_preprocess.py", line 280, in
worker.getSeq()
File "/usr/local/lib/python3.5/dist-packages/scikit-ribo/gtf_preprocess.py", line 154, in getSeq
self.fiveUtrDic[geneName] + self.fastaDic[geneName] + self.threeUtrDic[geneName] + "\n")
KeyError: 'ENSG00000230989'
This appears to be because in the 3utr.fasta, 5tr.fasta and cds.fasta files that were created have, for example, the following as a header:
ENSG00000187961::1:960586-965715(+)
Whereas the variable self.geneNames stores the IDs as only e.g. ENSG00000187961
Given the previous issue that I raised and solved, please can you confirm whether there is a problem in the code that is giving rise to this error?
Many thanks,
Catherine