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<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>
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cite="mid:622c5207-60a9-136a-f420-c66c1e960068@ebi.ac.uk">
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<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>
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cite="mid:25469e48-d7ce-4e0c-69cb-db527f7c5331@ebi.ac.uk">
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<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>
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cite="mid:66af20b2-39e9-701b-d208-f45fbcdc7e23@ebi.ac.uk">
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<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>
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cite="mid:a7228afe-5355-bd36-8a93-7617f98e4eff@ebi.ac.uk">
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<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>
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