<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<p>Hi Brandon,</p>
<p>Apologies for the delay but I have finally had time to make the
changes and open a PR
(<a class="moz-txt-link-freetext" href="https://github.com/Ensembl/ensembl/pull/407">https://github.com/Ensembl/ensembl/pull/407</a>).</p>
<p>Please let me know should there be any issues. I can confirm that
I have used my version of the code and it now works as expected.</p>
<p>Best wishes,<br>
Asier<br>
</p>
<div class="moz-cite-prefix">On 26/06/2019 11:35, Brandon Walts
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:6c456e1e-a812-ea04-3041-c50ae22fe1fc@ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<p>Hi Asier</p>
<p>It's great to hear that you've devised a fix. We would welcome
a PR against master, or to see your changes, whichever you'd
prefer. We'll be able to look at it in the next few days.<br>
</p>
<p>Best<br>
-Brandon<br>
</p>
<div class="moz-cite-prefix">On 26/06/2019 11:03, Asier Gonzalez
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:af0f2e81-0841-9f50-f5c0-01d9388d8c29@ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html;
charset=UTF-8">
<p>Hi Brandon,</p>
<p>Thank you for your response. Do you have an idea of when it
could be fixed? I mean, are we talking about weeks or months?
I use a tool that calls this function at least every two
months so I have amended the code to do what I believe it is
supposed to do. I could share it with you if it would help
you, or I could open a PR if you accept them. I understand
that you may have other priorities, but at least I want to
make sure that the future version will do what mine already
does.</p>
<p>Best wishes,<br>
Asier<br>
</p>
<div class="moz-cite-prefix">On 26/06/2019 10:56, Brandon Walts
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:622c5207-60a9-136a-f420-c66c1e960068@ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html;
charset=UTF-8">
<p>Hi Asier</p>
<p>We've had a chance to look into it and you are correct,
this function is not working as described. As currently
implemented, it will return more results than expected. It's
on our list to fix, and we plan to get to it in the near
future.</p>
<p>Best<br>
-Brandon<br>
</p>
<div class="moz-cite-prefix">On 26/06/2019 09:51, Asier
Gonzalez wrote:<br>
</div>
<blockquote type="cite"
cite="mid:25469e48-d7ce-4e0c-69cb-db527f7c5331@ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html;
charset=UTF-8">
<p>Hi Brandon,</p>
<p>Do you have any updates about this?</p>
<p>Thanks,<br>
Asier<br>
</p>
<div class="moz-cite-prefix">On 07/06/2019 16:42, Brandon
Walts wrote:<br>
</div>
<blockquote type="cite"
cite="mid:66af20b2-39e9-701b-d208-f45fbcdc7e23@ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html;
charset=UTF-8">
<p>Hi Asier</p>
<p>Thanks for bringing this up. We will look into what's
going on and see if there is a bug, if the documentation
needs improvement, or both.</p>
<p>Best<br>
-Brandon<br>
</p>
<div class="moz-cite-prefix">On 07/06/2019 13:47, Asier
Gonzalez wrote:<br>
</div>
<blockquote type="cite"
cite="mid:a7228afe-5355-bd36-8a93-7617f98e4eff@ebi.ac.uk">
<meta http-equiv="content-type" content="text/html;
charset=UTF-8">
<p>Hi all,</p>
<p>I'm troubleshooting a Perl tool that calls the
Ensembl API with a variant id and tries to find the
gene with the closest 5' end within a 500 kb window.
The tool was written by a colleague and it uses
Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_outward_search()
like this:</p>
<pre style="background-color:#ffffff;color:#000000;font-family:'Menlo';font-size:9.0pt;"><span style="color:#000080;font-weight:bold;">my </span>@gene_list_for_feature = @{$gene_adaptor->fetch_all_by_outward_search(
-FEATURE => $var_feature,
-RANGE => <span style="color:#0000ff;">10000</span>,
-MAX_RANGE => <span style="color:#0000ff;">500000</span>,
-LIMIT => <span style="color:#0000ff;">40</span>,
-FIVE_PRIME => <span style="color:#0000ff;">1</span>)};</pre>
<p>According to the documentation of this function (<a
class="moz-txt-link-freetext"
href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1BaseFeatureAdaptor.html#a76a51bc70828aaccb9435eda9a44b20a"
moz-do-not-send="true">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1BaseFeatureAdaptor.html#a76a51bc70828aaccb9435eda9a44b20a</a>),
it "Searches for features within the suggested -RANGE,
and if it finds none, expands the search area until it
satisfies -LIMIT or hits -MAX_RANGE". My understanding
is that in my case it should search first in a 10 kb
window and, if there are no genes, progressively
expand it to up to 500 kb unless it finds 40 features
before. However, this is not the behaviour I am
seeing, the search range grows like this: 10k, 20k,
60k, 240k and 1.20M. Is this a bug or have I
misundertood what it does?</p>
<p>I have looked into the code of this subroutine (<a
moz-do-not-send="true"
href="https://github.com/Ensembl/ensembl/blob/release/96/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm#L1441-L1469">https://github.com/Ensembl/ensembl/blob/release/96/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm#L1441-L1469</a>)
and the search window growths exponentially because it
multiplies the previous value instead of the initial
value:</p>
<p><span class="pl-smi">[L1452] $search_range</span> = <span
class="pl-smi">$search_range</span> * <span
class="pl-smi">$factor</span>;</p>
<p>In addition, it is not true that it only expands the
range if it does not find any features in the initial
window, which is obvious from looking into the while
statement:</p>
<p>[L1451] <span class="pl-k">while</span> (<span
class="pl-c1">scalar</span> <span class="pl-smi">@results</span>
< <span class="pl-smi">$limit</span> && <span
class="pl-smi">$search_range</span> <= <span
class="pl-smi">$max_range</span>) {</p>
<p>I am also confused by the fact that, apparently, the
found features only need to be partially within the
range. For instance, ENSG00000150394 (CDH8) is found
with the above parameters although its 5' prime end is
1,338,771 bp away from the variant according to the
distance reported by the function. So, it seems that
the feature is found because its 3' end is within the
range although the 5' prime end, which is what I am
interested in, is not. This somehow contradicts what
the documentation says (<a moz-do-not-send="true"
href="https://github.com/Ensembl/ensembl/blob/release/96/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm#L1490-L1491">https://github.com/Ensembl/ensembl/blob/release/96/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm#L1490-L1491</a>):
"When looking beyond the boundaries of the source
Feature, the distance is measured to the nearest end
of that Feature to the nearby Feature's nearest end."</p>
<p>Any help will be much appreciated. I am happy to
share code if you think it would be useful.</p>
<p>Thanks,<br>
Asier<br>
</p>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org" moz-do-not-send="true">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" moz-do-not-send="true">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/" moz-do-not-send="true">http://www.ensembl.info/</a>
</pre>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</body>
</html>