troubleshooting: error on run of kissplice2refgenome

Question

[celine]

I'm following a modified version of the pipeline outlined at http://kissplice.prabi.fr/tools/kiss2rt/ Except, that I have a reference genome.

Thus, I'm using kissplice2refgenome (and also I skip the trinity/transdecoder steps).

I've generated my .psl file through blat, and downloaded the annotations file in gtf format from http://genome.ucsc.edu/cgi-bin/hgTables.

With the following command,

kissplice2refgenome myPSLfile.psl myAnnotationsFile.gtf -o myOutputFile

I get the following error:

Run starts...
Reading annotations file...
Processing mapping information...
Traceback (most recent call last):
  File "/usr/local/bin/kissplice2refgenome", line 4, in <module>
    __import__('pkg_resources').run_script('kissplice2refgenome==1.0.0', 'kissplice2refgenome')
  File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 719, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 1511, in run_script
    exec(script_code, namespace, namespace)
  File "/usr/local/lib/python2.7/dist-packages/kissplice2refgenome-1.0.0-py2.7.egg/EGG-INFO/scripts/kissplice2refgenome", line 140, in <module>

  File "/usr/local/lib/python2.7/dist-packages/kissplice2refgenome-1.0.0-py2.7.egg/EGG-INFO/scripts/kissplice2refgenome", line 119, in main

TypeError: getInfoFile() takes exactly 18 arguments (16 given)

Thanks in advance for your help!

[celine]

Some more information:

My .psl file was generated with BLAT (I couldn't get the other options to work)

My annotations was downloaded from http://genome.ucsc.edu/cgi-bin/hgTables (http://bit.ly/2iDUiFB)

Answer 1

[leandro.ishi.lima]

Hello,

Maybe this is a command-line error, I am not sure. Could you please try the following run:

kissplice2refgenome -a myAnnotationsFile.gtf -o myOutputFile myPSLfile.psl

If this still does not work, maybe it is a good idea to try with a .sam file. Transform your psl to sam using samtools/misc/psl2sam.pl (https://github.com/samtools/samtools) and try:

kissplice2refgenome -a myAnnotationsFile.gtf -o myOutputFile mySAMfile.sam

If it does not work even like this, please tell us.

Kind regards.