[ensembl-dev] (no subject)

[Maria Xenophontos]

>
> Dear developer,
>
> I am using API version 67 and my aim is to retrieve feature sets for 3
> specific cell types (IMR90, MRC5, TIG3). I try to do so by fetching the
> cell type by name and then fetching the feature set by CellType. The script
> works fine for the IMR90 cell type, however when I try to get the cell type
> object for MRC5 or TIG3 I get an error for uninitialized value. I have also
> tried to create a cell type object as follows:
>

my $ctype_2= $ct_adaptor->fetch_all();
print STDOUT "**". $ctype_2->display_label()."\n";

  in order to check whether I should be passing 'MRC-5' instead of 'MRC5',
but again i get an error message for   calling display_label on an
unblessed reference.

I use the following script:

>
> my $ct_adaptor= $registry->get_adaptor('Human', 'funcgen', 'celltype');
> my $ctype_1= $ct_adaptor->fetch_by_name("IMR90");
>  my @fsets;
> my $fset_adaptor = $registry->get_adaptor( 'Human', 'funcgen',
> 'featureset' );
> my $fsets_1= $fset_adaptor->fetch_all_by_CellType($ctype_1);
> push @fsets, @{$fsets_1};
>
           #Works fine till here

        my $ctype_2= $ct_adaptor->fetch_by_name("MRC5");
>         my $fsets_2= $fset_adaptor->fetch_all_by_CellType($ctype_2);
>         push @fsets, @{$fsets_2};
>
>    I would really appreciate any comments and help on this. Thank you very
much.

P.S.: Please ignore my previous e-mail as it was accidentally sent to you
incomplete.

    Kind Regards,
    Maria Xenophontos

On Fri, Jul 20, 2012 at 2:12 PM, Maria Xenophontos <
m.xenophontos.cy at gmail.com> wrote:

> Dear developer,
>
> I am using API version 67 and my aim is to retrieve feature sets for 3
> specific cell types (IMR90, MRC5, TIG3). I try to do so by fetching the
> cell type by name and then fetching the feature set by CellType. The script
> works fine for the IMR90 cell type, however when I try to get the cell type
> object for MRC5 or TIG3 I get an error for uninitialized value
>
> my $ct_adaptor= $registry->get_adaptor('Human', 'funcgen', 'celltype');
> my $ctype_1= $ct_adaptor->fetch_by_name("IMR90");
>  my @fsets;
> my $fset_adaptor = $registry->get_adaptor( 'Human', 'funcgen',
> 'featureset' );
>  my $fsets_1= $fset_adaptor->fetch_all_by_CellType($ctype_1);
> push @fsets, @{$fsets_1};
>   my $ctype_2= $ct_adaptor->fetch_by_name("MRC5");
>  #print STDOUT "**". $ctype_2->display_label()."\n";
>  my $fsets_2= $fset_adaptor->fetch_all_by_CellType($ctype_2);
>  push @fsets, @{$fsets_2};
>
> --
> *Maria Xenophontos, BA
> MSc Student *
> School of Biological Sciences
> University of Edinburgh
>
>


-- 
*Maria Xenophontos, BA
MSc Student *
School of Biological Sciences
University of Edinburgh
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