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Dear Maartje,<br>
Sorry for the late reply.<br>
The feature you are printing are the introns, you will need to call
the method get_all_Exons from a transcript object, and you will need
to look at the exon boundaries to see which exon correspond to an
intron.<br>
<br>
The extra number you that is printed correspond to the sum of all
the intron spanning reads.<br>
<br>
Regards<br>
Thibaut<br>
<br>
<div class="moz-cite-prefix">On 22/11/12 09:39,
<a class="moz-txt-link-abbreviated" href="mailto:J.vandeVorst@gen.umcn.nl">J.vandeVorst@gen.umcn.nl</a> wrote:<br>
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<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">Dear
Thibaut,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">I
appreciate your quick response. I now have an idea how to
get the number of spanning reads, but I have another
question. Because I would like to have the number of
spanning reads per gene, I fetch the dna features that
overlap the gene and count all the reads as you can see in
the code below. But as I print the feature IDs, I see only
introns. Why are there no exons? And sometimes a big number
of reads is shown, like 1728.44444444444. Is this an
artefact or something?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">Regard
Maartje<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">#!/usr/bin/env
perl<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">use
strict;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">use
warnings;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">use
Bio::EnsEMBL::DBSQL::DBAdaptor;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">#
Connection to the rnaseq database<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">my
$rnaseqdb = new Bio::EnsEMBL::DBSQL::DBAdaptor(<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
-host => 'ensembldb.ensembl.org',<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
-port => 5306,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
-user => 'anonymous',<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
-dbname => 'homo_sapiens_rnaseq_69_37');<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">#
The GeneAdaptor and the DnaFeatureAdaptor are needed<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">my
$rnaseqsa = $rnaseqdb->get_SliceAdaptor();<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">my
$rnaseqaa = $rnaseqdb->get_AnalysisAdaptor();<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">my
$rnaseqdafa = $rnaseqdb->get_DnaAlignFeatureAdaptor();<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">foreach
my $slice (@{$rnaseqsa->fetch_all('toplevel')}) {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
foreach my $analysis (@{$rnaseqaa->fetch_all()}) {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
# To analyse with a logic name<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
my $logic_name = $analysis->logic_name;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
next if ($logic_name !~ /rnaseq/);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
print 'Looking at genes from analysis: ', $logic_name, "\n";<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
# To load the gene<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
foreach my $gene (@{$slice->get_all_Genes_by_type(undef,
$logic_name, 1)}) {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
print $gene->display_id, ':', $gene->start, ':',
$gene->end, ':', $gene->strand, ' on chromosome ',
$gene->seq_region_name, "\n";<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
# Rnaseq models have only one transcript per gene<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
foreach my $transcript (@{$gene->get_all_Transcripts()})
{<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
print $transcript->display_id, ':',
$transcript->start, ':', $transcript->end, ' length:
', $transcript->length, "\n";<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"> my
$tslice = $transcript->feature_Slice();<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
# To fetch the dna features that overlap the gene<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
my $features = $rnaseqdafa->fetch_all_by_Slice($tslice);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
my $read_count = 0;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
foreach my $feature (@{$features}) {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
print "\t", $feature->display_id, ':',
$feature->seq_region_start, ':',
$feature->seq_region_end, "\tNumber of spanning reads: ",
$feature->score, "\n";<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
# To count all the reads that span over a splice site<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
$read_count += $feature->score;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
print "\tNumber of spanning reads: ", $read_count, "\n";<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
print "\n";<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">
}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">Van:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">
<a class="moz-txt-link-abbreviated" href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a class="moz-txt-link-freetext" href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>]
<b>Namens </b>Thibaut Hourlier<br>
<b>Verzonden:</b> 19 November 2012 17:18<br>
<b>Aan:</b> <a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
<b>Onderwerp:</b> Re: [ensembl-dev] The number of
spanning reads for all genes<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Dear Maartje,<br>
First I have to warn you that for next release which is due in
January we will update the models of the RNASeq data for
human. These models have been generated with the improved
pipeline.<br>
<br>
It is "normal" that you can't get what you want because of the
way we put the data in the database. You will need to use a
DnaAlignFeatureAdaptor.<br>
Did you have a look at the perl script on this thread: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/pipermail/dev/2012-September/008071.html">
http://lists.ensembl.org/pipermail/dev/2012-September/008071.html</a>.
It's not exactly what you're trying to do but it is similar
and it shows a way of getting the number of spanning reads. It
is stored as the score of the DnaAlignFeature linked to the
exons.<br>
<br>
Regards<br>
Thibaut<o:p></o:p></p>
<div>
<p class="MsoNormal">On 19/11/12 13:39, <a
moz-do-not-send="true"
href="mailto:J.vandeVorst@gen.umcn.nl">
J.vandeVorst@gen.umcn.nl</a> wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hello Ensemble team,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">I was trying to get
the number of spanning reads for one gene by using the API
and the database homo_sapiens_rnaseq_69-37. I used the
following Perl code, but I didn’t get any results. The API
version I use is 69 and I would like to get the number of
spanning reads for all genes. I hope you can help me.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"><br>
Thank you!</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Regards Maartje</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">use
Bio::EnsEMBL::DBSQL::DBAdaptor;</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">$db = new
Bio::EnsEMBL::DBSQL::DBAdaptor(</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> -host
=> 'ensembldb.ensembl.org',</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> -port
=> 5306,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> -user
=> 'anonymous',</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">
-dbname => 'homo_sapiens_core_69_37',</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">
-species => 'Homo_sapiens');</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">$ga =
$db->get_GeneAdaptor();</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">$gene =
$ga->fetch_by_stable_id("ENSG00000109061");</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">$slice =
$gene->slice;</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">$rnaseqdb = new
Bio::EnsEMBL::DBSQL::DBAdaptor(</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> -host
=> 'ensembldb.ensembl.org',</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> -port
=> 5306,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> -user
=> 'anonymous',</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">
-dbname => 'homo_sapiens_rnaseq_69_37');</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">$rnaseqsa =
$rnaseqdb->get_SliceAdaptor();</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">$rnaseqslice =
$rnaseqsa->fetch_by_name($slice->name);</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">@transcripts =
@{$rnaseqslice->get_all_Transcripts('skeletal_rnaseq')};</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">foreach my $transcript
(@transcripts) {</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> foreach my $sf
(@{$transcript->get_all_supporting_features()}) {</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> #The number of
reads that spanned accross the intron</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> print STDOUT
$sf->hit_name, ' :', $sf->score, "\n";</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> }</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">}</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><br clear="all">
<o:p></o:p></span></p>
<p><span
style="font-size:10.0pt;font-family:"Arial","sans-serif"">Het
UMC St Radboud staat geregistreerd bij de Kamer van
Koophandel in het handelsregister onder nummer 41055629.<br>
The Radboud University Nijmegen Medical Centre is listed
in the Commercial Register of the Chamber of Commerce
under file number 41055629.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><o:p></o:p></pre>
<pre>Posting guidelines and subscribe/unsubscribe info: <a moz-do-not-send="true" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><o:p></o:p></pre>
<pre>Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><o:p> </o:p></span></p>
</div>
<br clear="all">
<p style="font-size:13px;font-family:arial;"> Het UMC St Radboud
staat geregistreerd bij de Kamer van Koophandel in het
handelsregister onder nummer 41055629.<br>
The Radboud University Nijmegen Medical Centre is listed in the
Commercial Register of the Chamber of Commerce under file number
41055629.<br>
</p>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
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