[ensembl-dev] accessing the tilepath entries programatically

Duarte Molha duartemolha at gmail.com
Tue Jun 30 15:46:36 BST 2015


no. That does not get anything.



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

On 30 June 2015 at 14:50, Thibaut Hourlier <thibaut at ebi.ac.uk> wrote:

> If you use name instead of clone_name, does it fetches the missing one?
>
> Cheers
> Thibaut
>
> On 30 Jun 2015, at 14:27, Duarte Molha <duartemolha at gmail.com> wrote:
>
> 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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