Kissplice2refgenome does not handle # in the very begining of GTF files
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Entering edit mode
4.1 years ago
Thibault D. ▴ 690

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 gtf RNA-Seq • 974 views
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Entering edit mode
2.3 years ago

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

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