[ensembl-dev] (no subject)

[Nathan Johnson]

HI Maria

Yes this is expected behaviour, we don't yet support MRC5 or TIG3 cell types. You are on the right tracks for finding out what we do store. I have edited you code below to print out all the stored cell type names:


> 	my @ctypes = @{$ct_adaptor->fetch_all()};
> 	map { print STDOUT "**". $_->name."\n" } @ctypes;


The 'unblessed reference' error was because you were trying to call a method on an array ref of CellType objects.

Hope this helps.

Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

http://www.ensembl.info/
http://twitter.com/#!/ensembl





On 20 Jul 2012, at 14:18, Maria Xenophontos 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. 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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