[ensembl-dev] accessing the tilepath entries programatically

[Duarte Molha]

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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