Error in running kissplice2reftranscriptome

Question

[c.evang]

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/pkg_resources.py", 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/pkg_resources.py", 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>
    main()
  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/outputFileWriter.py", 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!

[lavender_412]

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

Thanks for your help!

Answer 1

[vincent.lacroix]

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; http://kissplice.prabi.fr/tools/kiss2rt/ Thanks for reporting the bug !

Vincent

Answer 2

[leandro.ishi.lima]

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.

[c.evang]

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

https://drive.google.com/open?id=0BxZ448pnAtJaTGpoNE9Cb2Y5bkE

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.