From 1d338160c31803bbf7897f8caad7c749cf2ba5cc Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 4 Oct 2004 15:56:43 +0000
Subject: [PATCH] first draft release
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 124 +++++++++++++-----
1 file changed, 88 insertions(+), 36 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 5727910366..8e2950e762 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -1,8 +1,15 @@
-package BasicMapper;
+package XrefMapper::BasicMapper;
use strict;
use DBI;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Translation;
+
+my $xref_host = "ecs1g";
+my $xref_port = 3306;
+my $xref_database = "ianl_test_xref";
+my $xref_user = "ensadmin";
+my $xref_password = "ensembl";
sub new {
@@ -15,12 +22,17 @@ sub new {
$self->host($host);
$self->port($port);
$self->dbname($dbname);
- $self->$user($user);
- $self->$password($password);
- $self->$dir($dir);
+ $self->user($user);
+ $self->password($password);
+ $self->dir($dir);
+
+
+ return $self;
}
+
+
sub dump_seqs{
my ($self, $slice) = @_;
$self->dump_ensembl($slice);
@@ -33,7 +45,8 @@ sub dump_xref{
my $sql = "select species_id from species where name = '".$self->species."'";
- my $sth = dbi()->prepare($sql);
+ my $dbi = $self->dbi();
+ my $sth = $dbi->prepare($sql);
$sth->execute();
my @row = $sth->fetchrow_array();
my $species_id;
@@ -59,10 +72,16 @@ sub dump_xref{
$sql .= " x.species_id = ".$species_id." ";
$sth = dbi()->prepare($sql);
$sth->execute();
+ my $i = 0;
while(my @row = $sth->fetchrow_array()){
+ $i++;
$row[1] =~ s/(.{60})/$1\n/g;
print XDNA ">".$row[0]."\n".$row[1]."\n";
+ if($i > 10){
+ goto ENDDNA;
+ }
}
+ENDDNA:
close XDNA;
open(XPEP,">".$self->dir."/xref_prot.fasta") || die "Could not open xref_prot.fasta";
@@ -72,10 +91,16 @@ sub dump_xref{
$sql .= " x.species_id = ".$species_id." ";
$sth = dbi()->prepare($sql);
$sth->execute();
+ $i = 0;
while(my @row = $sth->fetchrow_array()){
+ $i++;
$row[1] =~ s/(.{60})/$1\n/g;
print XPEP ">".$row[0]."\n".$row[1]."\n";
+ if($i > 10){
+ goto ENDXPEP;
+ }
}
+ENDXPEP:
close XPEP;
}
@@ -102,57 +127,68 @@ sub fetch_and_dump_seq{
-host => $self->host(),
-port => $self->port(),
-password => $self->password(),
- -username => $self->username(),
+ -user => $self->user(),
-group => 'core');
- open(FILE,">".$self->ensembl_dna_file())
+ open(DNA,">".$self->ensembl_dna_file())
|| die("Could not open dna file for writing: ".$self->ensembl_dna_file."\n");
- $gene_adap = $reg->get_adaptor($self->species(),'core','Gene');
- my @genes = @{$gene_adap->list_dbIDs()};
- foreach my $gene (@genes){
+ open(PEP,">".$self->ensembl_protein_file())
+ || die("Could not open dna file for writing: ".$self->ensembl_protein_file."\n");
+
+ my $gene_adap = $db->get_GeneAdaptor();
+ my @gene_ids = @{$gene_adap->list_dbIDs()};
+ my $i =0;
+ foreach my $gene_id (@gene_ids){
+ $i++;
+ my $gene = $gene_adap->fetch_by_dbID($gene_id);
+ print "gene ".$gene."\n";
foreach my $transcript (@{$gene->get_all_Transcripts()}) {
my $seq = $transcript->spliced_seq();
$seq =~ s/(.{60})/$1\n/g;
- print FILE ">" . $transcript->dbID() . "\n" .$seq."\n";
+ print DNA ">" . $transcript->dbID() . "\n" .$seq."\n";
+ my $trans = $transcript->translation();
+ my $translation = $transcript->translate();
+ print "tranlation ".$translation."\n";
+ my $pep_seq = $translation->seq();
+ $pep_seq =~ s/(.{60})/$1\n/g;
+ print PEP ">".$trans->dbID()."\n".$pep_seq."\n";
+ }
+ if($i > 10){
+ goto FIN;
}
}
- close FILE;
-
- #now do the translations.
-
+FIN:
+ close DNA;
+ close PEP;
}
-# @transcript_ids = @{$transcript_adaptor->list_dbIDs()};
-# $transcript = $transcript_adaptor->fetch_by_dbID($trans_id);
-
+sub ensembl_protein_file{
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_ens_prot_file} = $arg );
+ return $self->{_ens_prot_file};
+}
+sub ensembl_dna_file{
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_ens_dna_file} = $arg );
+ return $self->{_ens_dna_file};
+}
-# $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
-# $slice_adaptor = $db->get_SliceAdaptor();
-#
-# $transcript_adaptor = $db->get_TranscriptAdaptor();
-#
-# $transcript = $transcript_adaptor->fetch_by_dbID(1234);
-#
-# $transcript = $transcript_adaptor->fetch_by_stable_id('ENST00000201961');
-#
-# $slice = $slice_adaptor->fetch_by_region('chromosome', '3', 1, 1000000);
-# @transcripts = @{$transcript_adaptor->fetch_all_by_Slice($slice)};
-#
-# ($transcript) = @{$transcript_adaptor->fetch_all_by_external_name('BRCA2')};
-
sub get_ensembl_type{
+ my %type;
- my %type; #
-
- my $type{'Translation'} = "peptide";
+ $type{'Translation'} = "peptide";
$type{'Transcript'} = "dna";
- return /%type;
+ return \%type;
}
sub species {
@@ -211,4 +247,20 @@ sub dir {
($self->{_dir} = $arg );
return $self->{_dir};
}
+
+
+sub dbi {
+
+ my $self = shift;
+
+ my $dbi = DBI->connect("dbi:mysql:host=$xref_host;port=$xref_port;database=$xref_database",
+ "$xref_user",
+ "$xref_password",
+ {'RaiseError' => 1}) || die "Can't connect to database";
+
+
+ return $dbi;
+}
+
+1;
--
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