Hi,<div><br></div><div>When I use the following code:</div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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<p class="p1">#!/usr/bin/perl</p>
<p class="p2"><br></p>
<p class="p1">use strict;</p>
<p class="p1">use Bio::EnsEMBL::Registry;</p>
<p class="p2"><br></p>
<p class="p1">my $reg = "Bio::EnsEMBL::Registry";</p>
<p class="p2"><br></p>
<p class="p1">$reg->load_registry_from_db( -host => '<a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a>', -user => 'anonymous' );</p>
<p class="p2"><br></p>
<p class="p1">my $exon_adaptor = $reg->get_adaptor( 'Bos taurus', 'Core', 'Exon' );</p>
<p class="p2"><br></p>
<p class="p1">my $exons = $exon_adaptor->fetch_all;</p>
<p class="p2"><br></p>
<p class="p1">print scalar( @{$exons} ), "\n";</p></div><div><br></div><div>I get:</div><div><br></div><div><div>farm2-head2[bert]2: perl <a href="http://test.pl">test.pl</a></div><div>225837</div><div><br></div>
<div>Which is the same number I get with a MySQL query:</div><div><br></div><div><div>mysql -u anonymous -h <a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a> -P 5306</div><div>Welcome to the MySQL monitor. Commands end with ; or \g.</div>
<div>Your MySQL connection id is 8610 to server version: 5.1.34-log</div><div><br></div><div>Type 'help;' or '\h' for help. Type '\c' to clear the buffer.</div></div><div><br></div><div><div>mysql> use bos_taurus_core_62_4k </div>
<div>Reading table information for completion of table and column names</div><div>You can turn off this feature to get a quicker startup with -A</div></div><div><div><br></div><div>Database changed</div></div><div><div>mysql> SELECT COUNT(*) FROM exon;</div>
<div>+----------+</div><div>| COUNT(*) |</div><div>+----------+</div><div>| 225837 |</div><div>+----------+</div><div>1 row in set (0.01 sec)</div></div><div><br></div><div>Cheers,</div><div>Bert</div><div><br></div><br>
<div class="gmail_quote">On Fri, May 6, 2011 at 4:22 PM, Andrea Edwards <span dir="ltr"><<a href="mailto:edwardsa@cs.man.ac.uk">edwardsa@cs.man.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff">
I tried 2 ways :<br>
<br>
===============================================<br>
<br>
my $gene_adaptor = $registry->get_adaptor( 'bos_taurus', 'Core',
'Gene' );<br>
my $genes = $gene_adaptor->fetch_all();<br>
<br>
my $exon_adaptor = $registry->get_adaptor( 'bos_taurus', 'Core',
'Exon' );<br>
$total_genes=0;<br>
$exon_count = 0;<br>
foreach $gene(@{$genes}) {<br>
$total_genes++;<br>
<br>
foreach $exon ($gene->get_all_Exons()) {<br>
$exon_count++;<br>
} <br>
} #end for each gene<br>
<br>
<br>
=============================================<br>
<br>
This way gave even less (23k) but i'm being stricter here about the
chromosomes<br>
<br>
@slices = @{ $slice_adaptor->fetch_all('chromosome', undef, 0, 1)
};<br>
<br>
$total_genes=0;<br>
$exon_count = 0;<br>
foreach $slice (@slices) {<br>
unless ($slice->seq_region_name() =~ /Un/) {<br>
print $slice->seq_region_name."\n";<br>
my $genes = $gene_adaptor->fetch_all_by_Slice($slice);<br>
<br>
<br>
foreach my $gene(@{$genes}) {<br>
$total_genes++;<br>
<br>
foreach my $exon ($gene->get_all_Exons()) {<br>
$exon_count++;<br>
print "$exon_count\n";<br>
} <br>
<br>
<br>
<br>
<br>
} #end for each gene<br>
}<br>
}<br>
<br>
==============================================<br>
<br>
But neither give anything like the sql results<br>
<br>
Why does the sql give so many more? Which should I use?<br>
<br>
thank you<div><div></div><div class="h5"><br>
<br>
<br>
On 06/05/11 15:50, Bert Overduin wrote:
<blockquote type="cite">Hi Andrea,
<div><br>
</div>
<div>I suspect that your BioMart results are truncated because the
query is too large.
<div><br>
</div>
<div>However, that doesn't explain your API results .... How
does your API code look like?<br>
<div><br>
</div>
<div>Cheers,</div>
<div>Bert<br>
<br>
<div class="gmail_quote">On Fri, May 6, 2011 at 3:45 PM,
Andrea Edwards <span dir="ltr"><<a href="mailto:edwardsa@cs.man.ac.uk" target="_blank">edwardsa@cs.man.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">Hello<br>
<br>
I'm sorry for the basic question but I was looking at
the ensembl core schema and trying to retrieve just the
exons on chromosomes and couldn't work out why i am
getting such different figures than with biomart and the
perl api<br>
<br>
For example for cow there are 25670 exons in genes with
biomart and the api but with this sql ~210k exons. This
code is just looking for exons on chromosomes 1-30 and X<br>
<br>
select count(distinct stable_id) from exon e inner join
exon_stable_id es using(exon_id) inner join seq_region
sr using(seq_region_id) where sr.coord_system_id = 2 and
<a href="http://sr.name" target="_blank">sr.name</a> REGEXP '^[1-9]|^X' and
e.is_current=1<br>
<br>
I get 8k just on chromosome 1<br>
<br>
I'm sure this is simple and perhaps its because its
Friday afternoon but I'm just not seeing it!!<br>
<br>
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</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Bert Overduin, Ph.D.<br>
Vertebrate Genomics Team<br>
<br>
EMBL - European Bioinformatics Institute<br>
Wellcome Trust Genome Campus<br>
Hinxton, Cambridge CB10 1SD<br>
United Kingdom<br>
<br>
<a href="http://www.ebi.ac.uk/%7Ebert" target="_blank">http://www.ebi.ac.uk/~bert</a>
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</blockquote></div><br><br clear="all"><br>-- <br>Bert Overduin, Ph.D.<br>Vertebrate Genomics Team<br><br>EMBL - European Bioinformatics Institute<br>Wellcome Trust Genome Campus<br>Hinxton, Cambridge CB10 1SD<br>United Kingdom<br>
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