k2rt couldn't deal with type3(indel) fasta?

Question

[ku1.heyi.92f]

Hello.

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 :

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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/__init__.py", 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/__init__.py", 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)

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

Answer 1

[vincent.lacroix]

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,

Vincent

[ku1.heyi.92f]

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

ku1.heyi.92f