Hi,
This may not be the 'best' way, but it I've found it to be a workable
solution.
I'm running a Perl script that takes the tool-xml parameters, does some processing,
and calls
R to obtain a p-val calculation. The results are parsed and included in a formatted HTML
page.
It's all code based.
You can likely use something similar in a Python script:
# --- create the R command
my $cmd=<<END;
echo 'phyper($match, $listcount, $all, $qrycount, lower.tail = FALSE, log.p =
FALSE)' > rcmd
END
system($cmd);
# --- run R in command line mode
my $runR=<<END;
R --slave -f rcmd > rpval
END
system($runR);
# --- open and parse results
open my $fh, "<", "rpval";
my $line = <$fh>;
close $fh;
$line =~ /\[1\] (.+)/;
hope you find this of use.
-ray
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