#430 Fix Percolator output columns

[William S Noble]

(1) The column "total matches/spectrum" should be "distinct matches/spectrum" or "total matches/spectrum", depending on what the input file contains. Currently, it is always reported as "total matches/spectrum."

(2) The posterior error probability produced by Percolator is not being reported in the output file. This should be in a column called "Percolator PEP."

[Kaipo]

For (1), what happens is that when we convert to pin, both distinct matches/spectrum and total matches/spectrum are used for lnNumSP. Then for output we look what the lnNumSP value was, but at that point we don't really know which one the value came from. Maybe we can have two different feature names so that they are distinguishable?

[William S Noble]

Just to confirm what we discussed in person, yes, you should use two
different feature names internally so that these are distinguishable.
Bill

On Wed, Sep 7, 2016 at 12:18 PM, Kaipo kaipot@users.sf.net wrote:

For (1), what happens is that when we convert to pin, both distinct
matches/spectrum and total matches/spectrum are used for lnNumSP. Then for
output we look what the lnNumSP value was, but at that point we don't
really know which one the value came from. Maybe we can have two different
feature names so that they are distinguishable?

---

• [issues:#430] https://sourceforge.net/p/cruxtoolkit/issues/430/ Fix
  Percolator output columns*

Status: open
Milestone: Crux v2.0
Labels: High priority
Created: Tue Sep 06, 2016 02:53 PM UTC by William S Noble
Last Updated: Tue Sep 06, 2016 02:53 PM UTC
Owner: Kaipo

(1) The column "total matches/spectrum" should be "distinct
matches/spectrum" or "total matches/spectrum", depending on what the input
file contains. Currently, it is always reported as "total matches/spectrum."

(2) The posterior error probability produced by Percolator is not being
reported in the output file. This should be in a column called "Percolator
PEP."

---

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[Kaipo]

Here is a patch to fix these two issues.

[William S Noble]

This looks good. All tests pass, and it seems to work well. Please check it
in.

On Thu, Sep 8, 2016 at 11:48 AM, Kaipo kaipot@users.sf.net wrote:

Here is a patch to fix these two issues.

Attachments:

• percolator_columns.diff
  https://sourceforge.net/p/cruxtoolkit/issues/_discuss/thread/9d87b669/197b/attachment/percolator_columns.diff
  (7.6 kB; text/x-patch)

---

• [issues:#430] https://sourceforge.net/p/cruxtoolkit/issues/430/ Fix
  Percolator output columns*

Status: open
Milestone: Crux v2.0
Labels: High priority
Created: Tue Sep 06, 2016 02:53 PM UTC by William S Noble
Last Updated: Wed Sep 07, 2016 07:18 PM UTC
Owner: Kaipo

(1) The column "total matches/spectrum" should be "distinct
matches/spectrum" or "total matches/spectrum", depending on what the input
file contains. Currently, it is always reported as "total matches/spectrum."

(2) The posterior error probability produced by Percolator is not being
reported in the output file. This should be in a column called "Percolator
PEP."

---

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https://sourceforge.net/p/cruxtoolkit/issues/430/

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[Kaipo]

Thanks Bill, it is committed (r17177)