[ensembl-dev] accessing the tilepath entries programatically
Duarte Molha
duartemolha at gmail.com
Fri Jul 3 17:01:24 BST 2015
Thanks Magali
Can you explain something to me?
You are now keeping the api compatible with both GRCH37 and GRCH38. This is
great because I can use my scripts with the latest API and not worry about
having to use an older API to query the older assembly. However I do not
understand why, in this case changing ‘clone_name’ to ‘Name’* works when
querying GRCh38 but fails when querying GRCh37.*
Shouldn't the API calls be the same for both datasets. This means I have
to change my code depending on what database I am querying. Isn't this what
the move to update the api for both datasets is trying to avoid?
Best regards
Duarte
=========================
Duarte Miguel Paulo Molha
http://about.me/duarte
=========================
On 2 July 2015 at 16:40, mag <mr6 at ebi.ac.uk> wrote:
> Hi Duarte,
>
> Replacing 'clone_name' with 'Name' as Thibaut suggested works for me for
> GRCh38.
>
> my $clones = $mf_adaptor->fetch_all_by_attribute_type_value( '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");
> }
>
>
> Regards,
> Magali
>
>
> On 01/07/2015 18:15, Duarte Molha wrote:
>
> I would still appreciate some help with this query. If possible.
> On 30 Jun 2015 16:29, "Duarte Molha" <duartemolha at gmail.com> wrote:
>
>> Thibaut... Could you expand on how I can change my script to make it
>> work with the new assembly?
>> I have just realised that the reason I am no getting 60 BAC entries is
>> because their are only present in GRCh38 and not on the GRCh37
>>
>> Can you tell me how I can modify my script to work with the new
>> assembly?
>>
>> I don't seem to understand the projection method you are using.
>> Here is the relevant part of my script
>>
>> 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 15:46, Duarte Molha <duartemolha at gmail.com> wrote:
>>
>>> 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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>>>>>>
>>>>>>
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