Simple way to get basecounts from pileup?

[JPreston]

Hello,

I have a problem that seems like it should be simple to solve but I am having difficulties. I need a way to print the basecounts for ~50 SNP positions in each of ~15 pileup files of different E. coli populations. I have tried using varscan readcounts, but the output is formatted irregularly, with the bases in a different order for each SNP, making it difficult to print the results of 15 different libraries to one file. (I have very beginner python skills).

It seems like there must be other options out there to do something as simple as this, but I haven't been able to find anything.

Any insights and advice about this would be greatly appreciated!!

Thanks!

-Jessica

[wolma]

Try pysam !
It will give you a nice API for doing what you want programmatically in Python.

Best,
Wolfgang