[ensembl-dev] accessing the tilepath entries programatically

[Duarte Molha]

Yes I am using the GRCh37 Thibaut  ... so I am ok for now... but it is good
to know this does not work with the latest assembly.
However... can you please answer my question regarding the missing clones
like  RP11-155D3 ... why can I not fetch this when it is clearly on the
database?

Thanks

Duarte



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

On 30 June 2015 at 14:12, Thibaut Hourlier <thibaut at ebi.ac.uk> wrote:

> My first question should have been which assembly are you using...
>
> So yes this will work for GRCh37. Unfortunately it will not work for
> GRCh38 but this is something that we will fix for release 82.
>
> So in the case of GRCh38, it is still possible but more complicated. It
> should work by getting the slice then projecting on the clone coordinate
> system
>
> $subSlice = $misc_clone->feature_Slice;
> $projectionSegment = $subSlice->project('clone')
>
> Cheers
> Thibaut
>
> On 30 Jun 2015, at 13:56, Duarte Molha <duartemolha at gmail.com> wrote:
>
> Nevermind... after searching for miscFeatures information I found the
> relevant part in the api tutorial
>
> Just for reference to anyone that has the same difficulties here is the
> relevant portion of the code I used:
> (please let me know if there is something I did wrong Thibaut)
>
> my $mf_adaptor         = $registry->get_adaptor( 'Human', 'Core',
> 'MiscFeature' );
>
> open (IN, ,"<", $options->{list})|| die "Could not open
> ".$options->{list}." for reading \n";
> my @input_queries = <IN>;
> close IN;
>
> foreach my $query (@input_queries){
> chomp $query;
> my $clones =  $mf_adaptor->fetch_all_by_attribute_type_value(
> 'clone_name', $query );
>
> while ( my $clone = shift @{$clones} ) {
> my $slice = $clone->slice();
> print join "\t", ("chr".$slice->seq_region_name(), $clone->start(),
> $clone->end() , $query."\n");
> }
> }
>
>
> Best regards
>
> Duarte
>
> =========================
>      Duarte Miguel Paulo Molha
>          http://about.me/duarte
> =========================
>
> On 30 June 2015 at 13:26, Duarte Molha <duartemolha at gmail.com> wrote:
>
>> 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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>>
>>
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