/usr/share/perl5/Bio/Tools/Run/Ensembl.pm is in libbio-perl-run-perl 1.7.1-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 | #
# BioPerl module for Bio::Tools::Run::Ensembl
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Ensembl - A simplified front-end for setting up the registry
for, and then using an Ensembl database with the
Ensembl Perl API.
=head1 SYNOPSIS
use Bio::Tools::Run::Ensembl;
# get a Bio::EnsEMBL::Gene for agene of interest
my $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
-name => 'BRCA2');
=head1 DESCRIPTION
This is a simple way of accessing the Ensembl database to retrieve gene
information. Rather than learn the whole Ensembl Perl API, you only need to
install it (that is, check it out from CVS:
http://www.ensembl.org/info/docs/api/api_installation.html
- ignore the information about BioPerl version) and then you can get information
about a gene using get_gene_by_name().
For gene retrieval it is especially useful compared to direct Ensembl Perl API
usage since it can use information from alternate data sources (orthologues,
Swissprot, Entrez) to get your gene.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Run::Ensembl;
use strict;
use Bio::WebAgent;
use Bio::DB::EUtilities;
use base qw(Bio::Root::Root);
our $ENSEMBL_INSTALLED;
our $NODB;
our $LOADED_STR;
our $TOTAL = 0;
our $ORTHS = 0;
our $SWISS = 0;
our $NCBI = 0;
our $BAD = 0;
our $GOOD = 0;
BEGIN {
eval {
require Bio::EnsEMBL::Registry;
};
$ENSEMBL_INSTALLED = ! $@;
$NODB = 0;
$LOADED_STR = '';
}
=head2 registry_setup
Title : registry_setup
Usage : Bio::Tools::Run::Ensembl->registry_setup(-host => $host,
-user => $user);
if (Bio::Tools::Run::Ensembl->registry_setup) {...}
Function: Configure the ensembl registy to use a certain database.
The database must be an Ensembl database compatible with the
Ensembl Perl API, and you must have that API installed for this
method to return true. Defaults to anonymous access to
ensembldb.ensembl.org
Or just ask if the registry is setup and the database ready to use.
Returns : boolean (true if Registry loaded and ready to use)
Args : -host => host name (defaults to 'ensembldb.ensembl.org')
-user => username (defaults to 'anonymous')
-pass => password (no default)
-port => port (defaults to 3306)
-db_version => version of ensembl database to use, if different from
your installed Ensembl modules
-verbose => boolean (1 to print messages during database connection)
-no_database => boolean (1 to disable database access, causing this
method to always return false)
=cut
sub registry_setup {
return 0 unless $ENSEMBL_INSTALLED;
my $class = shift;
my ($host, $user, $pass, $port, $verbose, $no_db, $db_version) =
$class->_rearrange([qw(HOST USER PASS PORT VERBOSE NO_DATABASE DB_VERSION)], @_);
$host ||= 'ensembldb.ensembl.org';
$user ||= 'anonymous';
$NODB = $no_db if defined($no_db);
return 0 if $NODB;
my $load_str = $host.$user. (defined $pass ? $pass : '') . (defined $port ? $port : '');
unless ($LOADED_STR eq $load_str) {
Bio::EnsEMBL::Registry->load_registry_from_db(-host => $host,
-user => $user,
defined $pass ? (-pass => $pass) : (),
defined $port ? (-port => $port) : (),
defined $db_version ? (-db_version => $db_version) : (),
-verbose => $verbose);
$LOADED_STR = $load_str;
}
return 1;
}
=head2 get_adaptor
Title : get_adaptor
Usage : my $adaptor = Bio::Tools::Run::Ensembl->get_adaptor($species, $type);
Function: Get a species-specific 'core' database adaptor, optionally of a
certain type.
Returns : Bio::EnsEMBL::DBSQL::DBAdaptor, OR if a certain type requested, a
Bio::EnsEMBL::DBSQL::${type}Adaptor
Args : Bio::Species or string (species name) (REQUIRED), AND optionally
string (the type of adaptor, eg. 'Gene' or 'Slice').
=cut
sub get_adaptor {
my ($class, $species, $type) = @_;
return unless $class->registry_setup;
return unless $species;
if (ref($species)) {
$species = $species->scientific_name;
}
return Bio::EnsEMBL::Registry->get_adaptor($species, 'core', $type) if $type;
return Bio::EnsEMBL::Registry->get_DBAdaptor($species, 'core');
}
=head2 get_gene_by_name
Title : get_gene_by_name
Usage : my $gene = Bio::Tools::Run::Ensembl->get_gene_by_name();
Function: Get a gene given species and a gene name. If multiple genes match
this combination, tries to pick the 'best' match.
Returns : Bio::EnsEMBL::Gene
Args : -species => Bio::Species or string (species name), REQUIRED
-name => string: gene name, REQUIRED
If searching for the supplied gene name in the supplied species
results in no genes, or more than one, you can choose what else is
attempted in order to find just one gene:
-use_orthologues => Bio::Species or string (species name), or array
ref of such things: see if any of these
supplied species have (unambiguously) a gene
with the supplied gene name and if a
(one-to-one) orthologue of that gene in that
species is present in the main desired species
supplied to -species, returns that orthologous
gene. (default: none, do not use orthologues)
-use_swiss_lookup => boolean: queries swissprot at expasy and if a
suitable match is found, queries ensembl with
the swissprot id. (default: 0, do not use
swiss)
-use_entrez_lookup => boolean: queries entrez at the NCBI server if
(only) a single gene could not be found by any
other method, then query ensembl with the
entrez gene id. (default: 0, do not use NCBI)
(Attempts proceed in this order and return as soon as one method is
successful.)
-strict => boolean: return undef with no warnings if more than one,
or zero genes were found. (default: 0, warnings are issued
and if many genes were found, one of them is returned)
=cut
sub get_gene_by_name {
my $class = shift;
return unless $class->registry_setup;
my ($species, $gene_name, $use_swiss, $use_orth, $use_entrez, $strict) =
$class->_rearrange([qw(SPECIES NAME
USE_SWISS_LOOKUP USE_ORTHOLOGUES
USE_ENTREZ_LOOKUP STRICT)], @_);
$species || $class->throw("You must supply a -species");
$gene_name || $class->throw("You must supply a -name");
my $taxid;
if (ref($species)) {
$taxid = $species->id;
$species = $species->scientific_name;
}
$TOTAL++;
#print ". ";
my $gene_adaptor = $class->get_adaptor($species, 'Gene') || return;
# get the first gene that matches our query, warn if more than one did
my @genes = @{$gene_adaptor->fetch_all_by_external_name($gene_name)};
my $gene = shift(@genes);
# if not good enough, try again using orthologues
if ($use_orth && (! $gene || @genes > 0)) {
my @tests;
if (ref($use_orth) && ref($use_orth) eq 'ARRAY') {
@tests = @{$use_orth};
}
else {
@tests = ($use_orth);
}
my $alias_species = Bio::EnsEMBL::Registry->get_alias($species);
foreach my $test_species (@tests) {
$test_species = $test_species->scientific_name if ref($test_species);
$test_species eq $species and next;
my $test_gene = $class->get_gene_by_name(-species => $test_species,
-name => $gene_name,
-strict => 1) || next;
my $homologue_results_ref = $test_gene->get_all_homologous_Genes();
# get the species and gene id of each homologue
foreach my $result_ref (@{$homologue_results_ref}) {
my ($homolog_gene, $homology, $homolog_species) = @{$result_ref};
# get_alias returns lower case, underscored version of what we get here
$homolog_species = lc($homolog_species);
$homolog_species =~ s/ /_/g;
$homolog_species eq $alias_species or next;
$homology->description eq 'UBRH' or next;
$gene = $homolog_gene;
$ORTHS++;
last;
}
$gene and last;
}
}
# if not good enough, try again using swissprot
if ($use_swiss && (! $gene || @genes > 0)) {
my $swiss_id;
#*** swiss look up should be farmed out to some dedicated class
my $swiss_name = lc($gene_name);
my $swiss_species = lc($species);
$swiss_species =~ s/\s/+/g;
my $url = "http://www.expasy.org/cgi-bin/get-entries?db=sp&db=tr&DE=&GNc=AND&GN=$swiss_name&OC=$swiss_species&view=&num=100";
my $web_agent = Bio::WebAgent->new();
$web_agent->url($url);
my $rq = HTTP::Request->new(GET=>$url);
my $reply = $web_agent->request($rq);
if ($reply->is_error) {
$class->throw($reply->as_string()."\nError getting for url $url!\n");
}
my $content = $reply->content;
if ($content && $content !~ /No entries have been found/) {
my @possibles = split("<tr><td><input type=checkbox name=ac value=", $content);
shift(@possibles);
my @good_ids;
foreach my $poss (@possibles) {
my ($id, $desc) = $poss =~ /^.+?<td>(.+?)<\/td>.+?<b>.+?<b>(.+?)<\/td>/;
unless ($desc =~ /Fragment/) {
push(@good_ids, $id);
}
}
if (@good_ids == 1) {
$swiss_id = shift(@good_ids);
}
}
if ($swiss_id) {
@genes = @{$gene_adaptor->fetch_all_by_external_name($swiss_id)};
$gene = shift(@genes);
$SWISS++ if ($gene && @genes == 0);
}
}
# if not good enough, try again with search for the gene name at ncbi
if ($use_entrez && (! $gene || @genes > 0)) {
my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch',
-db => 'gene',
-term => $taxid ? "$gene_name ${taxid}[taxid]" : "$gene_name \"$species\"[Organism]",
-usehistory => 'y',
-verbose => -1);
my $esummary = Bio::DB::EUtilities->new(-eutil => 'esummary',
-history => $esearch->next_History);
eval {$esummary->parse_data;};
if (!$@) {
my $ncbi_id;
while (my $docsum = $esummary->next_DocSum) {
my $item = $docsum->get_Item_by_name('Name');
if (lc($item->get_content) eq lc($gene_name)) {
$ncbi_id = $docsum->get_id;
last;
}
}
if ($ncbi_id) {
@genes = @{$gene_adaptor->fetch_all_by_external_name($ncbi_id)};
$gene = shift(@genes);
$NCBI++ if ($gene && @genes == 0);
}
}
}
if (@genes > 0) {
return if $strict;
#$class->warn("Species '$species' had multiple matches to gene '$gene_name', using first gene '".$gene->display_id."'");
}
unless ($gene) {
return if $strict;
$BAD++;
#$class->warn("Species '$species' didn't have gene '$gene_name'");
return;
}
$GOOD++;
return $gene;
}
sub _stats {
print "$TOTAL | $ORTHS | $SWISS | $NCBI | good vs bad = $GOOD vs $BAD\n";
}
1;
|