File: README.test

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profbval 1.0.22-6
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Notes on how this package can be tested.
────────────────────────────────────────

This package can be tested by executing

    sh installation-test

in order to confirm its integrity.

This test can write to stderr following message:

    Can't exec "pp_popcon_cnt": No such file or directory at /usr/bin/profbval line 6. 
    The Rost Lab recommends you install the pp-popularity-contest package that 
    provides pp_popcon_cnt:

    sudo apt-get install pp-popularity-contest

This appears when associated package named `pp-popularity-contest` is not 
installed. Other output to stderr must be absent.

To test manually, cd to some dir where you have write permissions and do
 
    cp -a /usr/share/doc/profbval/examples/* .
    profbval cad23.f cad23-fil.rdbProf cad23-fil.hssp result.profbval 9 6

There is also cad23.profbval.gz file provided in examples folder. 
Script `installation-test` also extracts it and compares it with 
result.profbval. If you want to check that everything goes as expected, 
you can unzip that file and compare it with the result of above profbval call.

Other notes 
───────────
This call is also valid:

  profbval cad23.f cad23-fil.rdbProf cad23-fil.hssp oo,o0,o1,o2,o3,o4,o5,o6,osn,osn2 9 -1,0,1,2,3,4,5,6,snap,snapfun

Providing 6 positional parameters is always mandatory (there is also 1 
additional parameter).

PROFbval can save results to different locations (not to current folder - works 
well with relative and absolute paths), however, it fails when directory of 
interest doesn't exist.

More details on parameters and output formats are available in the package's man 
page (run `man profbval`) or can be found in associated articles [1]. 

Man page describes how to generate HSSP input file. If you wonder, how to get rdbProf 
file, Rost Lab's PROFbval Wiki page [2] suggests following procedure:
  
  Generating an rdbProf file requires generating an HSSP input file. The HSSP 
  input file is used as input to the prof program.
    
    prof <filtered_hssp_file> both numresMin=17 nresPerLineAli=60 riSubSec=4 riSubAcc=3 fileRdb=<rdbProf_file>

Mentioned `prof` program is a part of `profphd` package listed in this package's
recommendations list.
 
References:

[1]: PROFbval-related articles, mentioned in package's debian/upstream/metadata
    http://www.ncbi.nlm.nih.gov/pubmed/16455751
    http://www.ncbi.nlm.nih.gov/pubmed/16080156
[2]: Rost Lab's PROFbval Wiki page
    https://rostlab.org/owiki/index.php/PROFbval