Hi Andrea,<div><br></div><div>Hi Andrea,<div><br></div><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
Hi<br><br>Is there an obvious way to get all of the introns for a gene or do I<br>have to keep track of the bases in between exons and work it out 'manually'<br><br>thanks</blockquote></div></div></div><div><br>Introns aren't explicitly defined in the EnsEMBL database and are instead built from the exons using the get_Introns() methods of the transcript object. As there can be multiple transcripts per gene, which share exons, retrieving all introns for all transcripts of a gene will return redundant data. The best way to get around this it to retrieve the canonical transcript using the gene object and then retrieve all introns from that.</div>
<div><br></div><div>For example you can set-up a gene adaptor and retrieve all gene stable ids using the list_stable_ids() method and then retrieve the canonical transcript for each gene stable id using the canonical_transcript() method and then call get_Introns() on the resulting transcriopt .</div>
<div><br></div><div>See the pdoc for more information <a href="http://www.ensembl.org/info/docs/Pdoc/ensembl/index.html">http://www.ensembl.org/info/docs/Pdoc/ensembl/index.html</a> on functionality that isn't listed in the main tutorial.</div>
<div><br></div><div>Cheers,</div><div><br>Steve</div><div><br><div class="gmail_quote">On 13 November 2010 12:00, <span dir="ltr"><<a href="mailto:dev-request@ensembl.org" target="_blank">dev-request@ensembl.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. list of chromosomes in an organism (Andrea Edwards)<br>
2. Re: list of chromosomes in an organism (simon andrews (BI))<br>
3. Re: list of chromosomes in an organism (Andrea Edwards)<br>
4. Re: list of chromosomes in an organism (Anne Parker)<br>
5. get all introns for a gene (Andrea Edwards)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 12 Nov 2010 14:36:39 +0000<br>
From: Andrea Edwards <<a href="mailto:edwardsa@cs.man.ac.uk" target="_blank">edwardsa@cs.man.ac.uk</a>><br>
Subject: [ensembl-dev] list of chromosomes in an organism<br>
To: <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Message-ID: <<a href="mailto:4CDD50F7.1020308@cs.man.ac.uk" target="_blank">4CDD50F7.1020308@cs.man.ac.uk</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
hi<br>
<br>
how do you get the list of chromosomes in an organism via the perl api?<br>
<br>
I ask because I'm trying to get the cow Z chromosome and can't access<br>
it. It is labelled MT in the genome browser so I have tried<br>
<br>
$slice = $slice_adaptor->fetch_by_region('chromosome','Z');<br>
$slice = $slice_adaptor->fetch_by_region('chromosome','MT');<br>
<br>
and neither work<br>
<br>
Thanks a lot<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 12 Nov 2010 14:52:31 +0000<br>
From: "simon andrews (BI)" <<a href="mailto:simon.andrews@bbsrc.ac.uk" target="_blank">simon.andrews@bbsrc.ac.uk</a>><br>
Subject: Re: [ensembl-dev] list of chromosomes in an organism<br>
To: dev ensembl <<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
Message-ID: <<a href="mailto:77C8A039-14A7-4ABC-98D3-F0580DA2B5FD@bbsrc.ac.uk" target="_blank">77C8A039-14A7-4ABC-98D3-F0580DA2B5FD@bbsrc.ac.uk</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
<br>
On 12 Nov 2010, at 14:36, Andrea Edwards wrote:<br>
<br>
> hi<br>
><br>
> how do you get the list of chromosomes in an organism via the perl api?<br>
<br>
We use:<br>
<br>
my @chr_slices = @{$db_adapter -> get_adaptor('slice') -> fetch_all('chromosome',undef,0,1)};<br>
<br>
You can then call $chr_slices[0]->seq_region_name() on each of the chr slices to get the actual name.<br>
<br>
Simon.<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Fri, 12 Nov 2010 14:52:42 +0000<br>
From: Andrea Edwards <<a href="mailto:edwardsa@cs.man.ac.uk" target="_blank">edwardsa@cs.man.ac.uk</a>><br>
Subject: Re: [ensembl-dev] list of chromosomes in an organism<br>
To: <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Message-ID: <<a href="mailto:4CDD54BA.2060008@cs.man.ac.uk" target="_blank">4CDD54BA.2060008@cs.man.ac.uk</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Hi<br>
<br>
I made a mistake in my last message, wasn't concentrating. I should have<br>
said:<br>
<br>
I have got a list of the chromosomes<br>
in the cow genome using the perl API and the 'Y' chromosome is named MT.<br>
However I can't retrieve this chromosome using either of the following<br>
<br>
$slice = $slice_adaptor->fetch_by_region('chromosome','Y');<br>
$slice = $slice_adaptor->fetch_by_region('chromosome','MT');<br>
<br>
The $slice is undefined<br>
<br>
I did this workaround to get chromsomes 1-29, X and MT<br>
<br>
@slices = @{ $slice_adaptor->fetch_all('chromosome') };<br>
foreach $slice (@slices) {<br>
<br>
unless ($slice->seq_region_name() =~ /Un/) {<br>
.....<br>
}<br>
}<br>
<br>
But i was curious why I couldn't get MT directly<br>
<br>
thanks<br>
<br>
<br>
On 12/11/2010 14:36, Andrea Edwards wrote:<br>
> hi<br>
><br>
> how do you get the list of chromosomes in an organism via the perl api?<br>
><br>
> I ask because I'm trying to get the cow Z chromosome and can't access<br>
> it. It is labelled MT in the genome browser so I have tried<br>
><br>
> $slice = $slice_adaptor->fetch_by_region('chromosome','Z');<br>
> $slice = $slice_adaptor->fetch_by_region('chromosome','MT');<br>
><br>
> and neither work<br>
><br>
> Thanks a lot<br>
><br>
> _______________________________________________<br>
> Dev mailing list<br>
> <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
> <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Fri, 12 Nov 2010 15:41:12 +0000<br>
From: Anne Parker <<a href="mailto:ap5@sanger.ac.uk" target="_blank">ap5@sanger.ac.uk</a>><br>
Subject: Re: [ensembl-dev] list of chromosomes in an organism<br>
To: Andrea Edwards <<a href="mailto:edwardsa@cs.man.ac.uk" target="_blank">edwardsa@cs.man.ac.uk</a>><br>
Cc: <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Message-ID: <<a href="mailto:AE514DA8-16C7-45B9-8EF1-92881697AF44@sanger.ac.uk" target="_blank">AE514DA8-16C7-45B9-8EF1-92881697AF44@sanger.ac.uk</a>><br>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br>
<br>
There is no Y chromosome in the cow genome, because the reference<br>
genome is female :)<br>
<br>
On 12 Nov 2010, at 14:52, Andrea Edwards wrote:<br>
<br>
> Hi<br>
><br>
> I made a mistake in my last message, wasn't concentrating. I should<br>
> have said:<br>
><br>
> I have got a list of the chromosomes<br>
> in the cow genome using the perl API and the 'Y' chromosome is named<br>
> MT. However I can't retrieve this chromosome using either of the<br>
> following<br>
><br>
> $slice = $slice_adaptor->fetch_by_region('chromosome','Y');<br>
> $slice = $slice_adaptor->fetch_by_region('chromosome','MT');<br>
><br>
> The $slice is undefined<br>
><br>
> I did this workaround to get chromsomes 1-29, X and MT<br>
><br>
> @slices = @{ $slice_adaptor->fetch_all('chromosome') };<br>
> foreach $slice (@slices) {<br>
><br>
> unless ($slice->seq_region_name() =~ /Un/) {<br>
> .....<br>
> }<br>
> }<br>
><br>
> But i was curious why I couldn't get MT directly<br>
><br>
> thanks<br>
><br>
><br>
> On 12/11/2010 14:36, Andrea Edwards wrote:<br>
>> hi<br>
>><br>
>> how do you get the list of chromosomes in an organism via the perl<br>
>> api?<br>
>><br>
>> I ask because I'm trying to get the cow Z chromosome and can't<br>
>> access it. It is labelled MT in the genome browser so I have tried<br>
>><br>
>> $slice = $slice_adaptor->fetch_by_region('chromosome','Z');<br>
>> $slice = $slice_adaptor->fetch_by_region('chromosome','MT');<br>
>><br>
>> and neither work<br>
>><br>
>> Thanks a lot<br>
>><br>
>> _______________________________________________<br>
>> Dev mailing list<br>
>> <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>> <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
><br>
><br>
> _______________________________________________<br>
> Dev mailing list<br>
> <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
> <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
<br>
Anne Parker<br>
Ensembl Web Production Manager<br>
<a href="http://www.ensembl.org" target="_blank">http://www.ensembl.org</a><br>
<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Sat, 13 Nov 2010 00:24:26 +0000<br>
From: Andrea Edwards <<a href="mailto:edwardsa@cs.man.ac.uk" target="_blank">edwardsa@cs.man.ac.uk</a>><br>
Subject: [ensembl-dev] get all introns for a gene<br>
To: <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Message-ID: <<a href="mailto:4CDDDABA.10603@cs.man.ac.uk" target="_blank">4CDDDABA.10603@cs.man.ac.uk</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Hi<br>
<br>
Is there an obvious way to get all of the introns for a gene or do I<br>
have to keep track of the bases in between exons and work it out 'manually'<br>
<br>
thanks<br>
<br>
<br>
<br>
------------------------------<br>
<br>
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<br>
End of Dev Digest, Vol 5, Issue 15<br>
**********************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>Kindest regards,<br><br>Steve Moss<br><a href="http://stevemoss.ath.cx" target="_blank">http://stevemoss.ath.cx</a><br>
</div>