[ensembl-dev] downloading exons

[Uma Maheswari]

Hi Gary,

Can you give us some more information about the problem, what version of 
API you are using and what is the error message you are getting? You can 
also download the full gene using biomart.

thanks
Uma


On 13/12/11 17:00, Gary Duncan wrote:
> I have the script below but it isnt quite working what did i do wrong?
> Plus can you get the entire length of the gene?
>
>
> use strict;
> use warnings;
> use Bio::EnsEMBL::Registry;
> use Bio::EnsEMBL::DBSQL::DBConnection;
> use Bio::EnsEMBL::Utils::SqlHelper;
>
> #Load all DBs from Ensembl Genomes
> Bio::EnsEMBL::Registry->load_registry_from_db(
>   -HOST => 'mysql.ebi.ac.uk <http://mysql.ebi.ac.uk>',
>   -PORT => 4157,
>   -USER => 'anonymous'
> );
>
> my $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new(
>   -HOST => 'localhost',
>   -PORT => 3306,
>   -USER => 'xxxxxx',
>   -PASS => 'xxxxxx',
>   -DBNAME => 'xxxxxx'
> );
> #Holds a soft reference to the DBConnection so we cannot combine the 
> two news
> my $h = Bio::EnsEMBL::Utils::SqlHelper->new(-DB_CONNECTION => $dbc);
>
> #Cleanup schema using do()
> $dbc->do('DROP TABLE IF EXISTS exon');
> $dbc->do(<<'SQL');
> CREATE TABLE exon (
>   idgld int(10) NOT NULL auto_increment,
>    stbl_id varchar(12),
>   seq_start varchar(12),
>   seq_stop varchar(12),
>   sequence text,
>   PRIMARY KEY(idgld)#)
> SQL
>
> #File management
> my $file = '/home/glduncan/data/intron.txt';
> if(-f $file) {
>   unlink $file or die "Cannot remove file '${file}': $!";
> }
>  open my $out, '>', $file or die "Cannot open ${file} for writing: $!";
>
> my $ids_file = '/home/glduncan/data/three4.txt';
> open my $fh, '<', $ids_file or die "Failed. Cannot open '${ids_file}' 
> for reading: $!";
> my $i = 1;
>
> #Get the adaptors once
> my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor('Dictyostelium 
> discoideum', 'core');
> my $gene_adaptor = $dba->get_GeneAdaptor();
>
> my @data;
>
> while(my $stable_id = <$fh>){
>     chomp $stable_id;
>     my $gene = $gene_adaptor->fetch_by_stable_id($stable_id);
>     foreach my $transcript (@{$gene->get_all_Transcripts()}) {
>       # print $out $transcript->stable_id(), "\n";
>         foreach my $exons (@{$transcript->get_all_Exons}) {
>         print $out $exons->seq_region_start.' - 
> '.$exons->seq_region_end.' - '.$exons->seq. "\n";
>           #Store into a temporary array
>           push(@data, [
>             $transcript->stable_id(),
>             $exons->seq_region_start(),
>             $exons->seq_region_end(),
>             $exons->seq()
>           ]);
>         }
>     }
> }
> close($fh) or die "Cannot close input file handle: $!";
>
> #Use the batch command from the helper to insert the data using only 
> one prepared statement
> my $dml = <<'SQL';
> INSERT INTO exon (stbl_id, seq_start, seq_stop, sequence)
> VALUES (?,?,?,?)
> SQL
> my $affected_rows = $h->batch(-DATA => \@data, -SQL => $dml);
> foreach my $row(@data){
>     foreach my $value(@$row){
>     print $value,'\n';
> }
> }
>
>
>
>
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