[ensembl-dev] accessing the tilepath entries programatically

Thibaut Hourlier thibaut at ebi.ac.uk
Tue Jun 30 13:15:37 BST 2015


Hi Duarte,
The clone names are stored in the misc_* tables. So you need to use the MiscFeatureAdaptor, http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1MiscFeatureAdaptor.html:

my $misc_clones = $mfa->fetch_all_by_Slice_and_set_code('tilepath');
foreach my $clone (@$misc_clones) {
 print join("\t", $clone->slice->seq_region_name, $clone->start, $clone->end, @{$clone->get_all_attribute_values('name')}), "\n";
}

A warning though, this is the tilepath so the boundaries of the clones are different from the contigs/clones in the assembly as sometimes they didn't use the entire clone for the assembly

Hope this help

Thibaut

> On 30 Jun 2015, at 11:50, Duarte Molha <duartemolha at gmail.com> wrote:
> 
> I used this code to get all the gebnomic coordinates of your subcontigs:
> 
> 
> my @slices = @{ $slice_adaptor->fetch_all('clone') };
> foreach my $slice (@slices){
> 	$progress->update();
> 	my $clone_name =  $slice->seq_region_name();
> 	my $projection = $slice->project('toplevel');
> 	foreach my $segment ( @{$projection} ) {
> 		my $to_slice = $segment->to_Slice();
> 		print join "\t", ("chr".$to_slice->seq_region_name(), $to_slice->start(), $to_slice->end(), $clone_name."\n"); 
> 	}
> }
> 
> However, by doing this, the database does not fetch the original clone name 
> 
> for example.. using this script I get 
> chr4    47567235        47733411        AC092597.1
> 
> However I would like to get :
> 
> chr4    47567235        47733411        RP11-100N21
> 
> Can someone explain what I am doing wrong?
> 
> Thanks
> 
> Duarte
> 
> 
> 
> =========================
>      Duarte Miguel Paulo Molha      
>          http://about.me/duarte         
> =========================
> 
> On 30 June 2015 at 09:45, Duarte Molha <duartemolha at gmail.com> wrote:
> Dear devs
> 
> How can I search for a specific clone id present on your tilepath
> 
> for example this: RP5-892C22
> 
> I would like to use the perl API if possible
> 
> Many thanks
> 
> Duarte
> 
> 
> 
> =========================
>      Duarte Miguel Paulo Molha      
>          http://about.me/duarte         
> =========================
> 
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