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Parse the NCBI taxonomy database with Perl !
By LEGE 1374 days ago
use Bio::DB::Taxonomy;
use warnings;
my $sps="human";
# Get one from a NCBI taxonomy database
my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile',
-directory=> "taxdump",
-nodesfile=> "taxdump/nodes.dmp",
-namesfile=> "taxdump/names.dmp");
#to check
#parseTax('homo_sapiens', 'metazoa');
#exit;
#my $nam = $dbh->get_taxon(-name => $sps);
$nam = $dbh->get_taxon(-taxonid => 9606);
if(!$nam) { print "Try again with correct scientific name\n"; exit;}
print "Eureka we found $sps, id is ", $nam->id, "\n"; # 9606
#$abc = $names{$speciesId};
my @taxa = $dbh->each_Descendent($nam);
#foreach (@taxa) {print $_->scientific_name ; print "--";}
my @taxa2 = $dbh->get_all_Descendents($nam);
#foreach (@taxa2) {print $_->scientific_name; print "**";}
#my $ancestor_taxon = $dbh->ancestor($nam); print "$ancestor_taxon->id ****";
#my $tree = $dbh->get_tree('human'); print $tree->name;
#print $nam->ancestor;
my $ancestor_taxon = $dbh->ancestor($nam);
#print $ancestor_taxon;
use Bio::Tree::Tree;
my $tree_functions = Bio::Tree::Tree->new();
my @lineage = $tree_functions->get_lineage_nodes($nam);
my $lineage = $tree_functions->get_lineage_string($nam);
#print $lineage;
foreach (@lineage) {print $_->scientific_name; print "\n";}
my $decision =recheck_class (1974465, "metazoa");
print $decision;
#It return 1 of matches otherwise 0 #case-insesitive
#Spelling mistake on classNode may leads to error
sub recheck_class {
my ($lineageId,$classNode)=@_;
use Bio::Tree::Tree;
my $tree_functions = Bio::Tree::Tree->new();
my $nam = $dbh->get_taxon(-taxonid => $lineageId);
my @lineage = $tree_functions->get_lineage_nodes($nam);
return 1 if ( grep { lc ($_->scientific_name) eq lc ($classNode)} @lineage )
}
