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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2007-09-21 22:52:22 UTC
  • mfrom: (1.2.2 upstream)
  • Revision ID: james.westby@ubuntu.com-20070921225222-tt20m2yy6ycuy2d8
Tags: 1.5.2.102-1
* Developer release.
* Upgraded source package to debhelper 5 and standards-version 3.7.2.
* Added libmodule-build-perl and libtest-harness-perl to
  build-depends-indep.
* Disabled automatic CRAN download.
* Using quilt instead of .diff.gz to manage modifications.
* Updated Recommends list for the binary package.
* Moved the "production-quality" scripts to /usr/bin/.
* New maintainer: Debian-Med packaging team mailing list.
* New uploaders: Charles Plessy and Steffen Moeller.
* Updated Depends, Recommends and Suggests.
* Imported in Debian-Med's SVN repository on Alioth.
* Executing the regression tests during package building.
* Moved the Homepage: field out from the package's description.
* Updated watch file.

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scripts/taxa/local_taxonomydb_query.PLS
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my $verbose = 0;
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my $plain   = 0;
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my ($nodesfile,$namesfile);
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my $idx_dir = '/tmp/idx';
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GetOptions('v|verbose' => \$verbose,
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           'nodes:s'   => \$nodesfile,
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           'names:s'   => \$namesfile,
 
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           'idx:s'     => \$idx_dir,
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           'h|help'    => sub{ exec('perldoc',$0);
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                                exit(0)
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                                } );
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    exec('perldoc',$0);
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    exit(0);
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}
 
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mkdir($idx_dir) unless -d $idx_dir;
 
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my $db = new Bio::DB::Taxonomy(-source    => 'flatfile',
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                               -nodesfile => $nodesfile,
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                               -namesfile => $namesfile,
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                               -directory => '/tmp/idx');
 
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                               -directory => $idx_dir);
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foreach my $sp ( @ARGV ) {
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    my $id = $db->get_taxonid($sp);
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    print "id is $id for $sp\n";
 
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    my $node = $db->get_Taxonomy_Node(-name => $sp);
 
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    if( defined $node ) {
 
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        print "id is ", $node->id, "\n"; # 9606
 
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        print "rank is ", $node->rank, "\n"; # species
 
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        print "scientific name is ", $node->scientific_name, "\n"; # Homo sapiens
 
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        print "division is ", $node->division, "\n"; # Primates
 
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    } else {
 
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        warn("no node found for query $sp");
 
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    }
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}
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=head1 NAME