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...