Error in parsing gtf file

[mzavolan]

Hello

I am trying to use ALFA on a yeast data set. I downloaded a gtf file from ENSEMBL, Saccharomyces_cerevisiae.R64-1-1.104.gtf, but I get a KeyError exception:

if "exon" in prev_features_minus[biotype]:                                                                                                                                                         

KeyError: 'snoRNA'

It doesn't seem to be an issue specific to snoRNAs, because if remove the snoRNA features from the gtf file the exception is raised for another annotation.

It seems that ALFA was run on yeast before, without raising such error. Any suggestions?

Thank you! Mihaela

[uniqueg]

You can get the file from here: http://ftp.ensembl.org/pub/release-104/gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.104.gtf.gz

[uniqueg]

I could reproduce the error with ALFA v1.1.1 from Conda with:

alfa -a Saccharomyces_cerevisiae.R64-1-1.104.gtf

However, after sorting with:

sort -k1,1 -k4,4n -k5,5nr GTF_FILE > SORTED_GTF_FILE

it works.

So it appears that the Ensembl yeast annotations, unlike those, e.g., for human and mouse, are not in the expected sort order, causing index builds to fail.

However, I think it would be nice if ALFA caught that and reported a more informative error message.

[mzavolan]

Thanks, it does work!

[mbahin]

Hi,

Thanks for your questions and solutions! :) I'm really sorry but have currently no time anymore to work on this. I hope the tools still helps...

Cheers, Mathieu