[Bioperl-pipeline] Annotation+Transformers

[bala]

On Thursday, March 20, 2003, at 10:00  AM, Juguang Xiao wrote:

>>
>>
>> So either I over kill the problem by attaching an iohandler to the 
>> Transformer and fetch the RawContig or attach a RawContigAdaptor to 
>> the converter
>> and fetch it using the original input id...any feelings?
>>
>
> I do not like this first way, since Transformer instance module should 
> be biopipe independant, at least the converter is. In general, 
> converter is just in charge of conversion, database information is 
> necessary.
>
> I also had such problem, Shawn, do you remember that I added 
> get_all_Contig_name in RawContigAdaptor in  my local code, and never 
> submit into ensembl because i am not sure if they like this 
> no-harm-but-not-necessary-for-them sub.  I prefer to have  2 own 
> module, rather than changing the ensembl code.
>

You mean creating another supplementary module?
Isn't neater to just add the subroutine to ensembl?
Its something that ensembl used to have anyway....


bala


> # My_EnsEMBL_DBSQL_DBAdaptor.pm
> package My_EnsEMBL_DBSQL_DBAdaptor;
> use strict;
> use Bio::EnsEMBL::DBSQL::DBAdaptor;
> use vars qw(@ISA);
> @ISA = qw(Bio::EnsEMBL::DBSQL::DBAdaptor);
>
> sub get_RawContigAdaptor{
>     my ($self) = @_;
>     return $self->_get_adaptor("My_EnsEMBL_DBSQL_RawContigAdaptor");
>
> }
> 1;
>
> # My_EnsEMBL_DBSQL_RawContigAdaptor.pm
> package My_EnsEMBL_DBSQL_RawContigAdaptor;
> use strict;
> use vars qw(@ISA);
> use Bio::EnsEMBL::DBSQL::RawContigAdaptor;
> @ISA = qw(Bio::EnsEMBL::DBSQL::RawContigAdaptor);
>
> =head2 get_all_Contig_name
>
>  Title   : get_all_Contig_id
>  Usage   :
>     my @contig_names = $obj->get_all_Contig_name;
>     my @contig_names = $obj->get_all_Contig_name(-limit => 5);
>     my @contig_names = $obj->get_all_Contig_name(-where => 
> $where_clause);
>
>  Function: returns all the valid (live) Contig ids in the database
>  Example :
>  Returns : an array of RawContig objects.
>  Args    :
>
> =cut
>
> sub get_all_Contig_name{
>    my ($self, @args) = @_;
>    my $sql = "select name from contig";
>    my ($limit, $where) = $self->_rearrange([qw(LIMIT WHERE)], @args);
>
>    $sql .= " where $where" if (defined $where);
>    $sql .= " limit $limit" if(defined $limit && $limit =~ /^\d+$/);
>
>    my $sth = $self->prepare($sql);
>    my $res = $sth->execute;
>    my @out;
>    while( my $rowhash = $sth->fetchrow_hashref) {
>        push(@out,$rowhash->{'name'});
>    }
>
>    return @out;
> }
> 1;
>
> Juguang
>
>
> Juguang Xiao
> Bioinformatics Engineer
> Computational Biology
> Temasek Life Sciences Laboratory
> 1 Research Link
> National University of Singapore
> Singapore 117604
>