[ensembl-dev] accessing the tilepath entries programatically
Duarte Molha
duartemolha at gmail.com
Tue Jul 7 10:24:47 BST 2015
Thanks Thibaut
what I want to know is: "the genomic coordinates of the clones in
assembly".
Cheers
Duarte
=========================
Duarte Miguel Paulo Molha
http://about.me/duarte
=========================
On 7 July 2015 at 09:55, Thibaut Hourlier <thibaut at ebi.ac.uk> wrote:
> Hi Duarte,
> Sorry for the late reply. This is not a problem with the API but a data
> problem.
> When you do the call $mf_adaptor->fetch_all_by_attribute_type_value(
> 'Name', $query ) you're asking for all the clones (misc features) which
> have the attribute 'Name'. So if we haven't store any data with this
> attribute, the API will return nothing but it will have done it's job. We
> used a different attribute in this case which was a error. It will be fixed
> for release 82. Sorry for the problem it's causing you.
>
> Before replying to your previous question about my code snippet, I may
> have misunderstood what you wanted to do. By printing the clone
> coordinates, do you want to know the coordinates of the clones in the
> assembly or do you want to know where the clones overlap the assembly (this
> is what the tilepath is)?
>
> Regards
> Thibaut
>
> On 7 Jul 2015, at 09:20, Duarte Molha <duartemolha at gmail.com> wrote:
>
> 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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