PeptideAtlas Pipeline Retool 2012/13

From SPCTools

10/29/12:

Why is the build pipeline so complex and time consuming? What are we trying to do?

1. Start with iPro and ProtPro results, refreshed to ref DB

=> We can skip refresh if ref DB same as search DB

2. For each expt, create PAidentlist template file with all PSMs above P=0.4; can be used for multiple builds on same data.

=> Why does this take so long?

3. Make combined, sorted PAIdentlist file

=> Can we speed the sorting? Currently we use unix sort.

=> What do we need APD files for?