[ensembl-dev] accessing the tilepath entries programatically
Thibaut Hourlier
thibaut at ebi.ac.uk
Tue Jun 30 14:50:13 BST 2015
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 <http://about.me/duarte>
> =========================
>
> On 30 June 2015 at 14:12, Thibaut Hourlier <thibaut at ebi.ac.uk <mailto: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 <mailto: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 <http://about.me/duarte>
>> =========================
>>
>> On 30 June 2015 at 13:26, Duarte Molha <duartemolha at gmail.com <mailto: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 <http://about.me/duarte>
>> =========================
>>
>> On 30 June 2015 at 13:15, Thibaut Hourlier <thibaut at ebi.ac.uk <mailto: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 <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 <mailto: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 <http://about.me/duarte>
>> > =========================
>> >
>> > On 30 June 2015 at 09:45, Duarte Molha <duartemolha at gmail.com <mailto: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 <http://about.me/duarte>
>> > =========================
>> >
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>>
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