[Bioperl-l] gerp++

kajendiran mahendiran kajendiran56 at googlemail.com
Tue Feb 28 05:57:03 EST 2012


Dear All,
         thank you for taking the time to look at my post. I am trying
to use the Bioperl module to analyse gerpelem output. I have used the
following code:

use Bio::Tools::Run::Phylo::Gerp;

my$parser = Bio::Tools::Phylo::Gerp->new(-file => "test.rates.elems");

while (my $feat = $parser->next_result()) {
    my ($start) = $feat->start();
    my ($end) = $feat->end();
    my ($rs_score) = $feat->score();
    my ($p_value) = ($feat->annotation->get_Annotations('p-value'))[0]-
>value();
    print $start, "\t", $end, "\t", $rs_score, "\t", $p_value, "\n";
}

The file I am trying to read is:
region	4850138	4850158	19.72	5.48888e-09	223119	0	0
region	221586	221606	19.72	5.48888e-09	223139	0	0
region	865234	865254	19.72	5.48888e-09	223159	0	0
region	4108337	4108490	42.8171	5.57134e-09	223312	0	0
region	2780908	2781050	42.5108	5.67614e-09	223454	0.1	4.3
region	3603457	3603637	42.9148	5.68931e-09	223634	0.1	4.3
region	995791	995961	42.9233	5.72716e-09	223804	0.1	4.3
region	1250933	1251094	42.8291	5.83297e-09	223965	0.1	4.3
region	4219830	4219941	40.856	5.97931e-09	224076	0.1	4.3
region	712708	712796	38.8442	6.04126e-09	224164	0.1	4.3
region	3170105	3170125	19.482	6.0786e-09	224184	0.1	4.3
region	3297610	3297802	42.563	6.08115e-09	224376	0.1	4.3
region	5296586	5296776	42.5578	6.14513e-09	224566	0.1	4.3
region	1400348	1400508	42.6387	6.30399e-09	224726	0.1	4.3
region	4103587	4103685	39.7477	6.48804e-09	224824	0.1	4.3
region	278040	278082	29.8649	6.50312e-09	224866	0.1	4.3
region	5449691	5449882	42.4149	6.58323e-09	225057	0.1	4.3
region	4435258	4435437	42.384	6.90672e-09	225236	0.1	4.3

The program runs without any errors but there is no print out. It
appears that the parser is undefined and I cannot seem to figure out
why. I am new to bioinformatics and I would appreciate any help. I am
trying to figure out what the columns correspond to in the gerpelems
output, the format does not correspond to the format given in the
manual for gerp++. There are additional numbers also in the .elems
file and I am not sure what they mean.

Thank you once again for your help.
Kajendiran


More information about the Bioperl-l mailing list