Question: k2rt couldn't deal with type3(indel) fasta?
gravatar for ku1.heyi.92f
2.8 years ago by
ku1.heyi.92f0 wrote:


By k2rt, I'm now trying to detect short indels (Not SNPs) which cause non-synonymous amino acid substitutions. I already get input files:

kissplice result (XXX_coherent_type_3.fa) kissDE result blat result file bed result file

But when I try to run k2rt, Type error occurs.

error message is :

Opening all files and formatting tables... Collecting data...

File ".../.pyenv/versions/2.7.10/bin/kissplice2reftranscriptome", line 4, in <module> __import__('pkg_resources').run_script('kissplice2reftranscriptomelib==1.3.2', 'kissplice2reftranscriptome') File ".../.pyenv/versions/2.7.10/lib/python2.7/site-packages/pkg_resources/", line 729, in run_script self.require(requires)[0].run_script(script_name, ns) File ".../.pyenv/versions/2.7.10/lib/python2.7/site-packages/pkg_resources/", line 1649, in run_script exec(script_code, namespace, namespace) File ".../.pyenv/versions/2.7.10/lib/python2.7/site-packages/kissplice2reftranscriptomelib-1.3.2-py2.7.egg/EGG-INFO/scripts/kissplice2reftranscriptome", line 577, in <module>

File ".../.pyenv/versions/2.7.10/lib/python2.7/site-packages/kissplice2reftranscriptomelib-1.3.2-py2.7.egg/EGG-INFO/scripts/kissplice2reftranscriptome", line 356, in main

TypeError: writeInMergedBubblesTsv() takes exactly 8 arguments (9 given)

I'd like to know whether indel analysis is possible by k2rt.

ADD COMMENTlink modified 2.8 years ago by vincent.lacroix130 • written 2.8 years ago by ku1.heyi.92f0
gravatar for vincent.lacroix
2.8 years ago by
vincent.lacroix130 wrote:

Dear User,

Unfortunately, k2rt does not support indels for now. This is something we are interested in developing, but we have nothing ready.

Best regards,


ADD COMMENTlink written 2.8 years ago by vincent.lacroix130

Thank you very much. I'm looking forward to new k2rt.


ADD REPLYlink written 2.8 years ago by ku1.heyi.92f0
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