Help with debugging input file

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Help with debugging input file

Postby onlyIDleft » Fri Mar 29, 2013 5:45 pm

I am using a bioinformatics pipeline composed of python scripts
available at http://shiulab.plantbiology.msu.edu/wik ... Pseudogene

Each set of input files is composed of a DNA file, protein file and a BLAST file from comparing these two (even if you dont follow what I am saying here about the type of files, it does not matter much I think)

Using a series of Python scripts, these input files are sequentially manipulated to get the final output. Some sets of input files work just fine, so I know the scripts in the pipeline work OK.

However, for some input files, the script BlastUtility.py gives an error. I need your help in figuring out
1. what in the input file(s) is/are causing this error
2. how to fix this (in a biologically acceptable manner)
3. to do steps 1 and 2 above and make sure that the pipeline runs OK and I obtain the final result

Could someone help me? I dont think this should take more than 30 minutes for an experienced programmer. The challenge here (as I've been told) is that the script was written by a biologist, and that it shows! :p

I was referred to this page from my original posting at http://python-forum.org/viewtopic.php?f=6&t=859&e=0 - that link will give you info on this specific script and the type of error...
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Re: Help with debugging input file

Postby metulburr » Fri Mar 29, 2013 6:08 pm

I was referred to this page from my original posting at viewtopic.php?f=6&t=859&e=0 - that link will give you info on this specific script and the type of error...
setrofim wrote:Narrowing down the problem any further will be difficult; partly because it can't be readily reproduced from what you've given


The problem is you never gave more info to better define the problem. We cant replicate it because it imports modules we dont have with the script you gave
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