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).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'