Issue 415: Transition list import should pick modified sequence column over bare sequence column

Status:closed
Assigned To:Guest
Type:Defect
Area:Skyline
Priority:3
Milestone:3.2
Opened:2015-05-14 by Brendan MacLean
Changed:2016-01-06 by Brendan MacLean
Resolved:2016-01-06 by Brendan MacLean
Resolution:Fixed
Closed:2016-01-06 by Brendan MacLean
2015-05-14 Brendan MacLean
Title»Transition list import should pick modified sequence column over bare sequence column
Assigned To»kaipot@u.washington.edu
Notify»collins
Type»Defect
Area»Skyline
Priority»3
Milestone»3.2
We now load the entire transition list into memory for transition list import and use a ModificationMatcher to guess modifications found in the the sequence column. However, we still have an issue where, if the transition list contains a bare sequence column before a modified sequence column, Skyline will use the bare sequence column and attempt to guess modification location with much less information than it could have if it used the modified sequence column.

Attached is a transition list from Ben Collins where this causes Skyline to guess methionine oxidation incorrectly. Now that we bring everything into memory, we should fix the code to find all usable sequence columns and then prioritize using a modified sequence column over a bare sequence column.
 
 test_library.tsv

2015-06-23 Brendan MacLean
Assigned Tokaipot@u.washington.edu»Brendan MacLean
I have fixed this locally to work with Ben's data here in Zurich. It is working nicely now.

2016-01-06 Brendan MacLean
resolve as Fixed
Statusopen»resolved
I fixed this a while ago. Works well.

2016-01-06 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest