#198 calibrate-scores does not follow the HTML spec

[William S Noble]

It appears that the HTML description of calibrate-scores is different from what the program actually does. The following differences should be eliminated.

1. The HTML says that there is a required argument specifying which column to extract the score from. This should instead be an optional parameter called "--score-column" where the default value is "XCorr score". Currently, the user has no control over which column is selected.

2. The program usage statement offers a --protein-database option. This option should be eliminated.

3. The HTML spec says the output files will be named calibrate-scores., but they are actually named qvalue.. The program behavior should be changed to match the spec.

[Kaipo]

Changes 2 and 3 are easy to make.
For change 1, the program also relies on the "xcorr rank" column, so the rank column might have to change with the score column. Also (though it is not mentioned in the documentation), the program can take pep.xml, sqt, or mzid as input in which case the score-column parameter would work differently.

[William S Noble]

OK, let's make changes 2 and 3, and then just updated the documentation to
make clear how the program chooses the columns/scores to use. We will be
revising this program extensively before too long, at which time we can fix
this.

Bill

On Mon, Sep 29, 2014 at 11:51 AM, Kaipo kaipot@users.sf.net wrote:

Changes 2 and 3 are easy to make.
For change 1, the program also relies on the "xcorr rank" column, so the
rank column might have to change with the score column. Also (though it is
not mentioned in the documentation), the program can take pep.xml, sqt, or
mzid as input in which case the score-column parameter would work
differently.

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• [issues:#198] http://sourceforge.net/p/cruxtoolkit/issues/198
  calibrate-scores does not follow the HTML spec*

Status: open
Milestone: post v2.0
Created: Tue Sep 23, 2014 11:32 PM UTC by William S Noble
Last Updated: Tue Sep 23, 2014 11:32 PM UTC
Owner: Kaipo

It appears that the HTML description of calibrate-scores is different from
what the program actually does. The following differences should be
eliminated.

1.

The HTML says that there is a required argument specifying which
column to extract the score from. This should instead be an optional
parameter called "--score-column" where the default value is "XCorr score".
Currently, the user has no control over which column is selected.
2.

The program usage statement offers a --protein-database option. This
option should be eliminated.
3.

The HTML spec says the output files will be named calibrate-scores.,
but they are actually named qvalue.. The program behavior should be
changed to match the spec.

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