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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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<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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<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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<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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