Question: Error in running kissplice2reftranscriptome
gravatar for c.evang
4.1 years ago by
c.evang10 wrote:

Dear All and kissplice-users, I'm run into an error when running kissplice2reftranscriptome; the error was:

Opening all files and formatting tables...
Collecting data...
Traceback (most recent call last):
  File "/usr/local/bin/kissplice2reftranscriptome", line 5, in <module>
    pkg_resources.run_script('kissplice2reftranscriptomelib==1.3.0', 'kissplice2reftranscriptome')
  File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.34-py2.7.egg/", line 505, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.34-py2.7.egg/", line 1245, in run_script
    execfile(script_filename, namespace, namespace)
  File "/usr/local/lib/python2.7/dist-packages/kissplice2reftranscriptomelib-1.3.0-py2.7.egg/EGG-INFO/scripts/kissplice2reftranscriptome", line 556, in <module>
  File "/usr/local/lib/python2.7/dist-packages/kissplice2reftranscriptomelib-1.3.0-py2.7.egg/EGG-INFO/scripts/kissplice2reftranscriptome", line 458, in main
    element[11], element[12], element[13])
  File "/usr/local/lib/python2.7/dist-packages/kissplice2reftranscriptomelib-1.3.0-py2.7.egg/kissplice2reftranscriptomelib/ioFilesActions/", line 63, in writeInMainTsvFileForSimpleSnp
    "\t" + readCountsVariant1 + "\t" + readCountsVariant2 + "\t" + str(isSpecificCondition) + "\n")
TypeError: cannot concatenate 'str' and 'list' objects

Thanks in advance for your help!

kissplice snp k2rt • 1.4k views
ADD COMMENTlink modified 4.0 years ago by vincent.lacroix130 • written 4.1 years ago by c.evang10
gravatar for vincent.lacroix
4.0 years ago by
vincent.lacroix130 wrote:

Dear Chiara and k2rt users, I apologise for my slow response on this forum. I had posted this message on the kissplice-users list, but I had forgotten to answer also on the forum. A new version of k2rt which solves this bug is now available here; Thanks for reporting the bug !


ADD COMMENTlink written 4.0 years ago by vincent.lacroix130
gravatar for leandro.ishi.lima
4.1 years ago by
leandro.ishi.lima90 wrote:

Dear Chiara,

Thanks for reporting this bug. Could you send us an input file, with your command-line, so that we can debug? Thanks !

Kind regards.

ADD COMMENTlink written 4.1 years ago by leandro.ishi.lima90

​​Dear Leandro, below the google drive link where the input files are deposited:

And this is the command-line I used for running k2rt:

kissplice2reftranscriptome -b assemblychec095n10_okay_okalt_newnames.fasta.transdecoder.bed -k results_mDr1_EcoC_mDr2_EcoC_mDr3_EcoC_WW1_EcoC_WW2_EcoC_WW3_EcoC_k25_coherents_type_0a.fa -t out_blat_SNP_on_transcripts_80.psl -s kissDE_output_C_pvalue05

Thank you very much.

ADD REPLYlink written 4.1 years ago by c.evang10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1442 users visited in the last hour