[ensembl-dev] accessing the tilepath entries programatically
Duarte Molha
duartemolha at gmail.com
Tue Jul 7 09:20:14 BST 2015
Anyone? Could you help me understand why the changing behavior of the same
API between datasets?
=========================
Duarte Miguel Paulo Molha
http://about.me/duarte
=========================
On 3 July 2015 at 17:01, Duarte Molha <duartemolha at gmail.com> wrote:
> 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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>>>>>>
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>>>>>>
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