ywan/viramp-project — pull request #2 by kdaily (2014-06-06 14:07:55+00:00)
Title: Fix genomeCMP.py resorting by target genome

I fixed the functionality to be able to sort the output of nucmer for genome comparison by the target genome contig/coordinates. This was not working due to pipes used in a chain of command line programs, which cannot be properly redirected when using subprocess.Popen. This solution does the reformatting (removing columns 5 and 6) and sorting (first by contig, then by the minimum start/end coordinate) in python using csv.DictReader and csv.DictWriter. I don't forsee any issues with large files, though I did not test this type of functionality.