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
|
#!/usr/bin/perl
## uses environment variable ENS pointing to the
## ENSEMBL API on the computer
use lib $ENV{ENS} || $ENV{PERL5LIB};
use IO::File;
use Getopt::Std;
use strict;
use warnings;
use Bio::EnsEMBL::ApiVersion;
use Bio::EnsEMBL::Registry;
## unification function for arrays
use List::MoreUtils qw/ uniq /;
my $script_version = "0.2.2";
## connecting to the ENSEMBL data base
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::ApiVersion;
my $user = "anonymous";
my $host = "ensembldb.ensembl.org";
my $port = 5306;
my $pass = "";
my $registry = 'Bio::EnsEMBL::Registry';
my $ensembl_version="none";
my $ensembl_database="core";
my $species = "human";
my $slice;
my $coord_system_version="unknown";
## get all gene ids defined in the database...
my @gene_ids = ();
my $gene_id = "ENSG00000109906";
$registry->load_registry_from_db(-host => $host, -user => $user,
-pass => $pass, -port => $port);
my $gene_adaptor = $registry->get_adaptor($species, $ensembl_database, "gene");
my $slice_adaptor = $registry->get_adaptor($species, $ensembl_database, "slice");
my $current_gene = $gene_adaptor->fetch_by_stable_id($gene_id);
print "Current gene: ".$current_gene->display_id()."\n";
my @transcripts = @{ $current_gene->get_all_Transcripts };
foreach my $transcript (@transcripts){
print "Current tx: ".$transcript->display_id()."\n";
my $transl = $transcript->translation();
if (defined($transl)) {
my $transl_id = $transl->stable_id();
print "Current translation ".$transl_id."\n";
my $attr = $transl->get_all_Attributes();
foreach my $a (@{$attr}) {
print "\tName: ", $a->name(), "\n";
print "\tCode: ", $a->code(), "\n";
print "\tDesc: ", $a->description(), "\n";
print "\tValu: ", $a->value(), "\n";
}
my @unip = @{ $transl->get_all_DBLinks('Uniprot%') };
if (scalar(@unip) > 0) {
foreach my $uniprot (@unip) {
my $unip_id = $uniprot->display_id();
##print UNIPROT "$transl_id\t$unip_id\n";
## OK, add also
## o uniprot_db: $uniprot->dbname();
## o uniprot_info: $uniprot->info_text();
my $dbn = $uniprot->dbname();
$dbn =~ s/Uniprot\///g;
my $descr = $uniprot->description();
my $infot = $uniprot->info_text();
my $stat = $uniprot->status();
my $infotype = $uniprot->info_type();
## mapping type.
print "uniprot: ".$unip_id."\n";
print " dbname: ".$dbn."\n";
print " info_text ".$infot."\n";
## Defines the method by which this ID was mapped (Uniprot ID was
## matched to the Ensembl protein ID).
print " info_type ".$infotype."\n";
}
}
}
}
|
