arq5x/poretools — pull request #38 by JohnUrban (2014-10-16 13:08:38+00:00)
Title: Qual v pos

Hi Nick/Aaron,

If interested, I added the "qualpos" subcommand and "qual_v_pos.py" to the repertoire. This allows the user to create boxplots of quality scores over subsequent positions/bins of all the reads. The plot reflects the length of the longest read considered, but obviously not every 3' position has the same number of quality scores considered as the initial 5' positions of the reads.

This allows one to view the quality score boxplots with --type as an option to do a more thorough analysis of quality vs position given read type.

Right now it also uses matplotlib and is therefore a part of poreminion. However, I will workout the rpy2 version in the coming days. I figured I would open the pull request now, if you wanted to glance at the code and test the functionality.

There is plenty to improve in terms of aesthetics, but for now it is great for exploratory data analysis.

best wishes,
John