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Revision 1.4 - (download) (annotate)
Tue Apr 24 14:57:31 2007 UTC (12 years, 7 months ago) by paarmann
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.3: +7 -0 lines
*** empty log message ***

use strict;
use warnings;
use LWP::Simple;
use CGI;

my $cgi = new CGI;
my $success = 0;

my $url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&report=sgml&id=". $cgi->param('id');
my $content = get($url);

my $genetic_code = "11";
if ($content =~ /\&lt\;GCId\&gt\;(.*)\&lt\;\/GCId\&gt\;/) {
    $genetic_code = $1;
}

my $lineage = "";
if ($content =~ /\&lt\;Lineage\&gt\;cellular organisms; (.*)\&lt\;\/Lineage\&gt\;/) {
    $lineage = $1;
    $success = 1;
}

my $domain = "";
if ($lineage =~ /^(Bacteria|Archaea)\;/) {
    $domain = $1;
}

my $genus = "";
if ($content =~ /\&lt\;ScientificName\&gt\;(.*)\&lt\;\/ScientificName\&gt\;(\W*)\&lt\;Rank\&gt\;genus\&lt\;\/Rank\&gt\;/) {
    $genus = $1;
}

my $species = "";
if ($content =~ /\&lt\;ScientificName\&gt\;(.*)\&lt\;\/ScientificName\&gt\;(\W*)\&lt\;Rank\&gt\;species\&lt\;\/Rank\&gt\;/) {
    $species = $1;
    $species =~ s/$genus\s//;
    $species =~ s/ii$/i/;
    $species =~ s/ae$/a/;
}

my $strain = "";
if ($content =~ /\&lt\;ScientificName\&gt\;(.*)\&lt\;\/ScientificName\&gt\;(\W*)\&lt\;OtherNames\&gt\;/) {
    $strain = $1;
    $strain =~ s/$genus\s//;
    $strain =~ s/$species\s//;
}

# if we didnt pick up a species and strain, it's likely that $strain contains the species
# example 1313 hasn't got a species taxon
unless ($species) {
       $species = $strain;
       $strain = '';
}

print $cgi->header();
if ($success) {
    print $lineage . "<br/>" . $genetic_code  . "<br/>" . $genus . "<br/>" . $species . "<br/>" . $strain . "<br/>" . $domain;
} else {
    print "not found";
}

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