Question: Kissplice2refgenome does not handle # in the very begining of GTF files
0
gravatar for Thibault D.
3.0 years ago by
Thibault D.690
European Union
Thibault D.690 wrote:

Hi,

I've been using Kissplice pipeline lately to perform personnal RNASeq analysis. As I used the pipeline described in the official Kissplice documentation, I've come across an error.

With the following command line:

kissplice2refgenome-1.0.0/kissplice2refgenome -a genomeDir/gencode.v24.chr_patch_hapl_scaff.annotation.gtf --pairedEnd True kiss_emt/star_coherents_type_1_Aligned.out.sam

I get the following output:

Run starts...
Reading annotations file...
Traceback (most recent call last):
  File "workdir/kissplice2refgenome-1.0.0/kissplice2refgenome", line 140, in <module>
    main()
  File "workdir/kissplice2refgenome-1.0.0/kissplice2refgenome", line 109, in main
    ssRef.readAnnotationFile(options.annotationFile)
  File "/workdir/kissplice2refgenome-1.0.0/kissplice2refgenomelib/spliceSitesRef.py", line 22, in readAnnotationFile
    self.getInfoAnnotationFile(event)
  File "workdir/kissplice2refgenome-1.0.0/kissplice2refgenomelib/spliceSitesRef.py", line 28, in getInfoAnnotationFile
    gettingAttributes=event[8].split(" ")

I just grepped out the headers in the GTF file to get rid of the error, as follows:

kissplice2refgenome-1.0.0/kissplice2refgenome -a <(cat genomeDir/gencode.v24.chr_patch_hapl_scaff.annotation.gtf | grep -vP "^#") --pairedEnd True kiss_emt/star_coherents_type_1_Aligned.out.sam

I was wondering if this was a known issue ? I just downloaded the GTF file from gencode, and did not perform any modification (aside from gunzip uncompression).

Thanks!

kissplice rna-seq gtf • 802 views
ADD COMMENTlink modified 14 months ago by vincent.lacroix130 • written 3.0 years ago by Thibault D.690
1
gravatar for vincent.lacroix
14 months ago by
vincent.lacroix130 wrote:

Dear Thibault,

Sorry for answering so late to this post, but yes this issue was corrected a long time ago now. Thanks for reporting it. The current version of k2rg is now 1.2.2 and you are welcome to try it.

Best,

Vincent

ADD COMMENTlink written 14 months ago by vincent.lacroix130
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