[ensembl-dev] accessing the tilepath entries programatically

[Duarte Molha]

Many thanks Thibaut

So... in regards to your question...

How can I query a specific clone and its correct coordinates if I know  the
clone ID.

For example

assuming this clone:
 RP11-100N21

In other words , how to I query the underlying clone dataset and output
those clones in genomic coordinates?

Many thanks

Duarte






=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================

On 30 June 2015 at 13:15, Thibaut Hourlier <thibaut at ebi.ac.uk> wrote:

> 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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