#221 Percolator command line option not valid in Windows binary

[Jeff Howbert]

The Sourceforge online documentation for Crux Percolator mentions this command line option:

--feature-in-file T|F – When set to T, the <search results=""> argument should be a tab-delimited file, in which the first row is a header, and each subsequent row is a PSM. The fields should be identifier, label (1 = target, -1 = decoy), feature1, ..., featureN, peptide, proteins. Default = F.</search>

In the latest Crux Windows binary, this option is not listed in the Percolator internal documentation. Furthermore, it is rejected as invalid if added to the command line.

[Kaipo]

I think this just needs to be removed from the documentation.

[Kaipo]

Jeff, you mentioned that make-pin was running even when you passed in a .pin file. Looking at PercolatorApplication.cpp, make-pin seems like it will only run if either list-of-files=T or the input file has extension "txt", "sqt", "pep.xml", or "mzid". Can you provide instructions on how to reproduce that behavior?

[Jeff Howbert]

Hi Kaipo,

I did further testing and it turns out I was mistaken about the file extension and invocation of make-pin. See my subsequent issue #224 for details. However, as explained in that issue, there are still some problems with Crux Percolator that limit my ability to use it for my crosslink project.

Jeff

[Jeff Howbert]

I have revisited the original problem in this Issue, i.e. the --feature-in-file command line option not being recognized. The new test used a Linux binary (rather than Windows) built from trunk on 3/11/15. The option is still not recognized. The following error message appears:

FATAL: Parameter 'feature-in-file' does not exist.

This matters because Bill asserts in Issue #224 that this option is the way to get Percolator to operate as a generic semi-supervised SVM classifier that ignores peptide and protein information.

Jeff

[Kaipo]

Jeff, can we close issue 224 and assign this one to me?

[Jeff Howbert]

Hi Kaipo,

I think we should leave #224 open until we know that addressing #221 actually fixes (or circumvents) the problems in #224. Yes, you can reassign #221 from me to yourself.

Jeff

On Mon, 23 Mar 2015, Kaipo wrote:

Jeff, can we close issue 224 and assign this one to me?

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** [issues:#221] Percolator command line option not valid in Windows binary**

Status: open
Milestone: Percolator
Labels: High priority
Created: Wed Dec 10, 2014 11:59 PM UTC by Jeff Howbert
Last Updated: Mon Mar 23, 2015 08:32 PM UTC
Owner: Jeff Howbert

The Sourceforge online documentation for Crux Percolator mentions this command line option:

--feature-in-file T|F – When set to T, the <search results=""> argument should be a tab-delimited file, in which the first row is a header, and each subsequent row is a PSM. The fields should be identifier, label (1 = target, -1 = decoy), feature1, ..., featureN, peptide, proteins. Default = F.</search>

In the latest Crux Windows binary, this option is not listed in the Percolator internal documentation. Furthermore, it is rejected as invalid if added to the command line.

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