[Bioperl-l] Taxonomy hierarchy extraction
George Heller
george.heller at yahoo.com
Tue Jun 19 00:29:31 UTC 2007
But the problem is that I don't really get any output on the screen. In the /tmp directory I get 4 files namely parents, nodes, id2names and names2id, but I dont know what to make of them. This is what my script looks 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;
my $namesfile;
my ($nodefile,$namesfile) = ('nodes.dmp','names.dmp');
my $db = new Bio::DB::Taxonomy(-source => 'flatfile',
-nodesfile => $nodefile,
-namesfile => $namesfile,
-directory => $idx_dir);
my $node = $db->get_Taxonomy_Node(-taxonid => '33090');
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
}
Thanks.
George
Jason Stajich <jason at bioperl.org> wrote:
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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Dept of Biochemistry
University of Illinois Urbana-Champaign
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