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SchulzLab / Aeron

Alignment, quantification and fusion prediction from long RNA reads
MIT License
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list index out of range when running GraphBuilder.py #15

Open noncodo opened 4 years ago

noncodo commented 4 years ago

Hello! Trying to generate a custom .gfa file but hitting this snag: 

$ python /home/apps/Aeron/AeronScripts/GraphBuilder.py -e /home/refs/human/dna/hg38_wControl.fa -g /home/refs/human/rna/gencode.v35wControl.annotation.gtf -o aeron_out`
Reading Sequences
Done reading sequences
Reading and processing gtf
Traceback (most recent call last):
  File "/home/apps/Aeron/AeronScripts/GraphBuilder.py", line 183, in <module>
    pg = ParseGTF(fn)
  File "/home/apps/Aeron/AeronScripts/ParseGTF.py", line 36, in __init__
    en[exn[0]].append(enu[0])
IndexError: list index out of range

Looks like a semantic issue with the latest gencode gtf, which doesn't have double quotes next to the exon_number values. removing the double quotes on line 36 of parseGTF.py fixed it.

ddurai commented 3 years ago

Dear noncodo,

Thanks for pointing out the problem. It was truly a semantic error. We will fix this in the new version