[Bioperl-l] Taxonomy hierarchy extraction

Jason Stajich jason at bioperl.org
Mon Jun 18 20:17:34 EDT 2007


All the children are in this array.

You get to decide what you want to do with them. In the following  
example I print the id, rank, and scientific name out to the screen.
Because this is a taxonomy db query you are getting back  
Bio::Taxonomy::Taxon objects so read the documentation for this  
module to see what you can do with the object.
I would also suggest spending a little time with the Getting started  
and HOWTO:Trees documentation on the website to get familiar with the  
objects and nomenclature.


my @extant_children = grep { $_->is_Leaf } $node->get_all_Descendents;

for my $child ( @extant_children ) {
   print "id is ", $child->id, "\n"; # NCBI taxa id
   print "rank is ", $child->rank, "\n"; # e.g. species
   print "scientific name is ", $child->scientific_name, "\n"; #  
scientific name
}

On Jun 18, 2007, at 5:04 PM, George Heller wrote:

> Ok, I installed the latest of Scalar::Util and the script seems to  
> be working. But I am confused where exactly I need to look for the  
> descendent taxon ids once the script is run. I did look into the / 
> tmp/ directory, but I couldnt understand much.
>
>   Sorry to be bothering, really appreaciate your patience.
>
>   Thanks.
>   George
>
> Jason Stajich <jason at bioperl.org> wrote:
>   Try installing the latest Scalar::Util
>     On Jun 18, 2007, at 4:05 PM, George Heller wrote:
>
>     This is the output of /usr/bin/perl -V
>
>
>   Summary of my perl5 (revision 5 version 8 subversion 5)  
> configuration:
>     Platform:
>       osname=linux, osvers=2.6.9-22.18.bz155725.elsmp,  
> archname=i386-linux-thread-multi
>       uname='linux hs20-bc1-4.build.redhat.com  
> 2.6.9-22.18.bz155725.elsmp #1 smp thu nov 17 15:34:08 est 2005 i686  
> i686 i386 gnulinux '
>       config_args='-des -Doptimize=-O2 -g -pipe -m32 -march=i386 - 
> mtune=pentium4 -Dversion=5.8.5 -Dmyhostname=localhost - 
> Dperladmin=root at localhost -Dcc=gcc -Dcf_by=Red Hat, Inc. - 
> Dinstallprefix=/usr -Dprefix=/usr -Darchname=i386-linux - 
> Dvendorprefix=/usr -Dsiteprefix=/usr -Duseshrplib -Dusethreads - 
> Duseithreads -Duselargefiles -Dd_dosuid -Dd_semctl_semun -Di_db - 
> Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio - 
> Dinstallusrbinperl -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/ 
> less -isr -Dinc_version_list=5.8.4 5.8.3 5.8.2 5.8.1 5.8.0'
>       hint=recommended, useposix=true, d_sigaction=define
>       usethreads=define use5005threads=undef useithreads=define  
> usemultiplicity=define
>       useperlio=define d_sfio=undef uselargefiles=define  
> usesocks=undef
>       use64bitint=undef use64bitall=undef uselongdouble=undef
>       usemymalloc=n, bincompat5005=undef
>     Compiler:
>       cc='gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DDEBUGGING - 
> fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE - 
> D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm',
>       optimize='-O2 -g -pipe -m32 -march=i386 -mtune=pentium4',
>       cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict- 
> aliasing -pipe -I/usr/local/include -I/usr/include/gdbm'
>       ccversion='', gccversion='3.4.6 20060404 (Red Hat 3.4.6-2)',  
> gccosandvers=''
>       intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
>       d_longlong=define, longlongsize=8, d_longdbl=define,  
> longdblsize=12
>       ivtype='long', ivsize=4, nvtype='double', nvsize=8,  
> Off_t='off_t', lseeksize=8
>       alignbytes=4, prototype=define
>     Linker and Libraries:
>       ld='gcc', ldflags =' -L/usr/local/lib'
>       libpth=/usr/local/lib /lib /usr/lib
>       libs=-lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil - 
> lpthread -lc
>       perllibs=-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
>       libc=/lib/libc-2.3.4.so, so=so, useshrplib=true,  
> libperl=libperl.so
>       gnulibc_version='2.3.4'
>     Dynamic Linking:
>       dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='- 
> Wl,-E -Wl,-rpath,/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE'
>       cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib'
>
>
>   Characteristics of this binary (from libperl):
>     Compile-time options: DEBUGGING MULTIPLICITY USE_ITHREADS  
> USE_LARGE_FILES PERL_IMPLICIT_CONTEXT
>     Built under linux
>     Compiled at Jul 24 2006 18:28:10
>     @INC:
>       /usr/lib/perl5/5.8.5/i386-linux-thread-multi
>       /usr/lib/perl5/5.8.5
>       /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi
>       /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi
>       /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi
>       /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi
>       /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi
>       /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>       /usr/lib/perl5/site_perl/5.8.5
>       /usr/lib/perl5/site_perl/5.8.4
>       /usr/lib/perl5/site_perl/5.8.3
>       /usr/lib/perl5/site_perl/5.8.2
>       /usr/lib/perl5/site_perl/5.8.1
>       /usr/lib/perl5/site_perl/5.8.0
>       /usr/lib/perl5/site_perl
>       /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi
>       /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi
>       /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi
>       /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi
>       /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi
>       /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>       /usr/lib/perl5/vendor_perl/5.8.5
>       /usr/lib/perl5/vendor_perl/5.8.4
>       /usr/lib/perl5/vendor_perl/5.8.3
>       /usr/lib/perl5/vendor_perl/5.8.2
>       /usr/lib/perl5/vendor_perl/5.8.1
>       /usr/lib/perl5/vendor_perl/5.8.0
>       /usr/lib/perl5/vendor_perl
>
>
>     Thanks.
>     George
>       .
>
>
>   Hilmar Lapp <hlapp at gmx.net> wrote:
>     The perl version appears to be 5.8.5 though, so something strange
>   appears to be going on too.
>
>
>   George, can you please post the output of
>
>
>   $ /usr/bin/perl -V
>
>
>   -hilmar
>
>
>   On Jun 18, 2007, at 6:33 PM, Chris Fields wrote:
>
>
>     As the error implies your local version of perl doesn't seem  
> support
>   weak references, which means it doesn't have Scalar::Utils (which  
> was
>   added to core after perl 5.6.1, I think). Try installing
>   Scalar::Utils to see what happens.
>
>
>   chris
>
>
>   On Jun 18, 2007, at 5:18 PM, George Heller wrote:
>
>
>     I tried running the below mentioned script and I seem to be  
> getting
>   the following error:
>
>
>   Weak references are not implemented in the version of perl at /
>   usr/lib/perl5/site_perl/5.8.5/Bio/Tree/Node.pm line 76
>   BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.5/
>   Bio/Tree/Node.pm line 76.
>   Compilation failed in require at my.pl line 7.
>   BEGIN failed--compilation aborted at my.pl line 7.
>
>
>   My script looks something like,
>
>
>   #!/usr/bin/perl
>   use strict;
>   #use warnings;
>   use DBI;
>   use Bio::Tree::Node;
>   use Bio::DB::Taxonomy;
>   use Bio::DB::Taxonomy::flatfile;
>   my $idx_dir = '/tmp';
>
>
>   my ($nodefile,$namesfile) = ('nodes.dmp','names.dmp');
>   my $db = new Bio::DB::Taxonomy(-source => 'flatfile',
>   -nodesfile => $nodesfile,
>   -namesfile => $namesfile,
>   -directory => $idx_dir);
>   my $node = $db->get_Taxonomy_Node(-taxonid => '33090');
>   my @extant_children = grep { $_->is_Leaf } $node-
>     get_all_Descendents;
>
>
>   foreach $field (@extant_children) {
>   print "$field";
>   print "|";
>   print "\n";
>   }
>
>
>   And I am running the script using the command,
>
>
>   perl myscript.pl -v --names names.dmp --nodes nodes.dmp
>
>
>   and I have the nodes.dmp and names.dmp files in the current
>   directory.
>
>
>   Thanks,
>   George
>
>
>
>
>   Jason Stajich wrote:
>   It is implemented in the implementing class - DB::Taxonomy is
>   just the base class. For example see the flatfile implementation
>   Bio::DB::Taxonomy::flatfile
>
>
>   See the scripts/taxa/local_taxonomydb_query.PLS for example using
>   it:
>   nodes and names are from NCBI taxonomy database.
>
>
>
>
>   Here is an un-debugged copy+paste for your question that *should*
>   work.
>
>
>
>
>   use Bio::DB::Taxonomy
>   my $idx_dir = '/tmp';
>
>
>
>
>   my ($nodefile,$namesfile) = ('nodes.dmp,'names.dmp');
>   my $db = new Bio::DB::Taxonomy(-source => 'flatfile',
>   -nodesfile => $nodesfile,
>   -namesfile => $namesfile,
>   -directory => $idx_dir);
>   my $node = $db->get_Taxonomy_Node(-taxonid => '33090');
>   my @extant_children = grep { $_->is_Leaf } $node-
>     get_all_Descendents;
>
>
>
>
>
>
>
>
>   -jason
>
>
>   On Jun 18, 2007, at 10:07 AM, George Heller wrote:
>
>
>   What exactly is the "node n" in the query below. When I issue
>   this query, it says,
>
>
>
>
>   relation "node" does not exist.
>
>
>
>
>   I tried to use the get_all_Descendents method but it looks like
>   in order to do a recursive call it calls the method
>   each_Descendent. This method is not implemented in
>   Bio::DB::Taxonomy. It just has a single line,
>
>
>
>
>   shift->throw_not_implemented();
>
>
>
>
>   Thanks.
>   George.
>
>
>
>
>   Hilmar Lapp wrote:
>   I'm a bit confused - it sounds like you have set up a local
>   BioSQL
>   database and loaded the NCBI taxonomy into the database. You can
>   now
>   use simple SQL to retrieve all descendants of a node in the tree
>   given its NCBI taxonID such as
>
>
>
>
>   SELECT tn.*, tnm.name FROM taxon tn, taxon_name tnm, node n
>   WHERE
>   n.ncbi_taxon_id = :taxonID
>   AND tn.left_value > n. left_value
>   AND tn.right_value < n.right_value
>   AND tn.taxon_id = tnm.taxon_id
>   AND tn.name_class = 'scientific_name'
>
>
>
>
>   BioPerl doesn't have a Taxonomy::biosql module yet (though this
>   would
>   seem like a worthwhile thing to add), so you can't use the
>   Bio::DB::Taxonomy interface to do this against a BioSQL instance.
>
>
>
>
>   However, BioPerl does have support for the flat-file download of
>   the
>   NCBI taxonomy database and indexes it, so you can simply use
>   Taxonomy::{get_taxon,get_all_Descendants} using the flatfile
>   download
>   to achieve what you wanted to do in a less than 5 lines of perl.
>
>
>
>
>   Although the recursive implementation of
>   Taxonomy::get_all_Descendants
>   () won't be lightning fast, it may still be perfectly fine for your
>   application - are you sure it is not?
>
>
>
>
>   -hilmar
>
>
>
>
>   On Jun 18, 2007, at 12:21 AM, George Heller wrote:
>
>
>
>
>   Thanks. And how can I assign the $node here in the below code,
>   such
>   that I can reference it to a particular taxon id record? I want to
>   retrieve all the descendents from the taxonomy hierarchy, given a
>   particular taxon id.
>
>
>
>
>   I have a local db setup, in which I have uploaded data using the
>   load_ncbi_taxonomy.pl script.
>
>
>
>
>   Thanks.
>   George
>
>
>
>
>   Jason Stajich wrote:
>   I assume you already figured out how to setup a local taxonomydb?
>
>
>
>
>
>
>
>
>   You just want the extant species/leaves of the tree
>
>
>
>
>
>
>
>
>   my @extant_children = grep { $_->is_Leaf } $node-
>     get_all_Descedents;
>
>
>
>
>
>
>
>
>
>
>
>
>   -jason
>   On Jun 17, 2007, at 11:41 AM, George Heller wrote:
>
>
>
>
>   Hi all,
>
>
>
>
>
>
>
>
>   Can anyone point me to some example that uses the
>   get_all_Descendents method from Bio::DB::Taxonomy? I am a newbie at
>   this, and I am not quite sure how to implement it.
>
>
>
>
>
>
>
>
>   Thanks.
>   George
>
>
>
>
>
>
>
>
>   Sendu Bala wrote:
>   George Heller wrote:
>   Hi all,
>
>
>
>
>
>
>
>
>   I am looking at extracting the taxonomy hierarchy for some taxon
>   ids.
>   What I plan to do is, for a given taxon id, say 33090, I want to
>   extract all taxon ids that are children of this species. I do not
>   just want the immediate children, but the children's children
>   and so
>   on.
>
>
>
>
>
>
>
>
>   Any ideas on the way I can go about doing this?
>
>
>
>
>
>
>
>
>   Well, you'll use Bio::DB::Taxonomy presumably, and
>   each_Descendent in
>   some kind of looping structure. Most easily a recursing sub.
>
>
>
>
>
>
>
>
>   If you happen to code up something neat and efficient, why not
>   share it
>   with us and we could add it to the Taxonomy module(s).
>
>
>
>
>
>
>
>
>
>
>
>
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>
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>
>
>
>
>
>
>
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>   --
>   Jason Stajich
>   jason at bioperl.org
>   http://jason.open-bio.org/
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>   : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
>   ===========================================================
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>   http://jason.open-bio.org/
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>   Christopher Fields
>   Postdoctoral Researcher
>   Lab of Dr. Robert Switzer
>   Dept of Biochemistry
>   University of Illinois Urbana-Champaign
>
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