KisSplice2RefGenome version 2.0.0 error ?

Question

[david.b.rombaut]

Hi !

After version 2.5 of KisSplice, the new version of KisSplice2RefGenome seems nice, but I can't manage to launch it. Typically, I would launch the previous version with :

kissplice2refgenome \
    -a /media/***/gencode.v19.annotation.gtf \
    -o /media/***/event.txt \
    --pairedEnd True \
    --readLength 76 \
    /media/***/MDS_mapped2GRCh37Aligned.out.sam

(** obviously to hide the path)

With the 1.2.3 version, it worked perfectly. But exact same command with 2.0 give me :

kissplice2refgenome: error: unrecognized arguments: /media/***/MDS_mapped2GRCh37Aligned.out.sam

I tried to move the sam to the same repertory as KisSplice2RefGenome (to remove the path), remove the ".out", put the command on a single line, but no.

Maybe I have missed something really obvious, but the --help doesn't indicate any change to how to indicate the input file, so I don't really know.

Does anybody have the same problem ?

Thanks in advance for your time and help !

EDIT: I should mention that this happened after I have installed 2.0.0 with python, and NOT python3. Which might be why this doesn't work. Still, it doesn't work either with python3, and as I am absolutely not fluent in python... :

Traceback (most recent call last):
File "/usr/local/bin/kissplice2refgenome", line 4, in <module>
__import__('pkg_resources').run_script('kissplice2refgenome==2.0.0', 'kissplice2refgenome')
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 658, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1445, in run_script
exec(script_code, namespace, namespace)
File "/usr/local/lib/python3.6/dist-packages/kissplice2refgenome-2.0.0-py3.6.egg/EGG- 
INFO/scripts/kissplice2refgenome", line 57, in <module>
ImportError: cannot import name 'Paths'

[david.b.rombaut]

Hi Audric,

I have effectively missed something, guess I wasn't attentive enough ! Not only does it work, but it is also far quicker and the number of (standard) events has increased by a good 20% (compared to the 1.2.3 version) on one of my smallest cohort. I definitely need to check that.

Thank you very much !

Answer 1

[audric.cologne]

Hi David !

The problem is the --pairedEnd parameter. Since version 2.0.0, users should not explicitly set this parameter to True, adding --pairedEnd is enough. The following command line should work :

kissplice2refgenome \
-a /media/***/gencode.v19.annotation.gtf \
-o /media/***/event.txt \
--pairedEnd \
--readLength 76 \
/media/***/MDS_mapped2GRCh37Aligned.out.sam

Does this fix solve your problem ?

Best,

Audric