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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.
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
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