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Hi Will,<br>
<br>
Awesome! ClinVar is so direct to check $tva->feature_seq with
$pf->risk_allele.<br>
<br>
As you said, for other PhenotypeFeatures like OMIM there's no
risk_allele, allele_symbol or allele_accession_id.<br>
<br>
<b>1 2228866 rs387907306 G A,T<br>
<br>
</b>For this case I'm getting two OMIM phenotype features I can't
"check" if correct since risk_allele association provides the OMIM
allelic variant number<b>. </b>I guess then there's no way to
associate OMIM phenotype feature to a specific allele.<br>
<b><br>
</b>
<blockquote><b><b># omim_feature: 1</b></b><br>
<b><b> </b></b>phenotype_description: Shprintzen-Goldberg
craniosynostosis syndrome<br>
source_name: OMIM<br>
external_reference: MIM:164780<br>
is_significant: 1<br>
variation allele: A<br>
The risk allele is: 0004<br>
</blockquote>
<b><b> </b></b>
<blockquote><b><b> # omim_feature: 2</b></b><br>
<b><b> </b></b>phenotype_description: Shprintzen-Goldberg
craniosynostosis syndrome<br>
source_name: OMIM<br>
external_reference: MIM:164780<br>
is_significant: 1<br>
variation allele: A<br>
The risk allele is: 0005<br>
<br>
<b> # omim_feature: 1</b><br>
<b> </b>phenotype_description: Shprintzen-Goldberg
craniosynostosis syndrome<br>
source_name: OMIM<br>
external_reference: MIM:164780<br>
is_significant: 1<br>
variation allele: T<br>
The risk allele is: 0004<br>
<b> </b><br>
<b> # omim_feature: 2</b><br>
<b> </b>phenotype_description: Shprintzen-Goldberg
craniosynostosis syndrome<br>
source_name: OMIM<br>
external_reference: MIM:164780<br>
is_significant: 1<br>
variation allele: T<br>
The risk allele is: 0005<br>
</blockquote>
<br>
<br>
Regards,<br>
Guillermo.<br>
<b> </b><br>
<div class="moz-cite-prefix">On 17/08/15 10:25, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX2jmybKwZQBuajzqJW+B+hK6De=OtiRyMJug=2Bqw8GuQ@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>The plugin run() sub-routine is executed for each allele +
transcript combination; the object is a
TranscriptVariationAllele, and you can find to which allele
you are referring with either $tva->variation_feature_seq()
or $tva->feature_seq(); these give you the allele relative
to the input variant and transcript respectively (i.e. the two
will differ if the transcript is on the reverse strand. See <a
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1TranscriptVariationAllele.html">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1TranscriptVariationAllele.html</a></div>
<div><br>
</div>
<div>The data you return from the run() sub will only appear in
the block of output for that allele.</div>
<div><br>
</div>
<div>If you are retrieving phenotype data from Ensembl, then you
may find that we don't always have an allele-specific
annotation stored. For some PhenotypeFeature objects, they
will have an attribute "risk_allele", "allele_accession_id" or
"allele_symbol", but many will not. You may also find that due
to strand or reporting issues, the sequence in the associated
allele may not match exactly one of the alleles from the
VariationFeature or VCF.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 14 August 2015 at 14:49, Guillermo
Marco Puche <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Dear devs,<br>
<br>
I would like to know what's the correct way to handle
information when multiple alleles appear in a VCF record.<br>
<br>
For example, Homo_sapiens_clinically_associated.vcf
dataset:<br>
<br>
<b>1 2228866 rs387907306 G A,T</b><br>
<br>
Each one of alternative alleles has different OMIM and
Clinvar allele info.<br>
<br>
The plugin code is using the following scope:<br>
<br>
<b>sub feature_types {</b><b><br>
</b><b> return ['Transcript'];</b><b><br>
</b><b>}<br>
<br>
</b>Is there another feature_type level like Transcript,
Allele?<b><br>
</b><br>
I'm trying to solve it with the iteration code you
provided me Will:<span class=""><br>
<br>
<b> foreach my $known_var(@{$vf->{existing} ||
[]}) {</b><b><br>
</b><b> foreach my
$pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})}){</b><b><br>
</b></span><b> #do_stuff</b><b><br>
</b><b> }</b><b><br>
</b><b>}</b><br>
<br>
However this is getting me the phenotype information for
both alternative alleles (A and T) (transcript level) and
this being wrote in output for every alternative allele
consequence twice. So I'm getting phenotype info of A,T
written in allele A consequences and in allele T
consequences.<br>
<br>
How can I get the phenotype informartion for each allele
sperately? I think Ensembl can handle this since in VCF
output consequences are separated not only by transcript
but also by alternative allele.<br>
<br>
Thank you,<br>
<br>
Best regards,<br>
Guillermo.
<div>
<div class="h5"><br>
<br>
<br>
<div>On 26/03/15 12:57, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">You will probably see odd behaviour
if you mix versions of the script / API / caches /
databases. Feel free to experiment, though we
can't support such setups obviously.
<div><br>
</div>
<div>It works fine for me on 75 or 79 (i.e. using
"git checkout --release 75" in ensembl-tools,
ensembl-variation, ensembl-core)</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 26 March 2015 at
11:26, Guillermo Marco Puche <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> I guess
it's a problem with my API installation
then.<br>
<br>
If I install latest API(79) and continue to
use <a moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a>
from version 75 will it continue working or
I'll get conflicts/weird behaviours?<br>
<br>
Thanks!<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<br>
<div>On 26/03/15 11:53, Will McLaren
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Example output (I set
$Data::Dumper::Maxdepth = 1;):
<div><br>
</div>
<div>> echo "rs699" | perl -I
~/Git/guillermo/vep/ <a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a>
-plugin Clinvar -data -force -db
75<br>
</div>
<div>
<div>2015-03-26 10:51:38 - Reading
input from STDIN (or maybe you
forgot to specify an input
file?)...</div>
<div>2015-03-26 10:51:38 -
Starting...</div>
<div>2015-03-26 10:51:38 -
Detected format of input file as
id</div>
<div>2015-03-26 10:51:38 - Read 1
variants into buffer</div>
<div>2015-03-26 10:51:38 -
Checking for existing variations</div>
<div>[===================================================================================================================================================================================================]
[ 100% ]</div>
<div>2015-03-26 10:51:38 - Reading
transcript data from cache
and/or database</div>
<div>[===================================================================================================================================================================================================]
[ 100% ]</div>
<div>2015-03-26 10:51:38 -
Retrieved 4 transcripts (0 mem,
0 cached, 4 DB, 0 duplicates)</div>
<div>2015-03-26 10:51:38 -
Analyzing chromosome 1</div>
<div>2015-03-26 10:51:38 -
Analyzing variants</div>
<div>[===================================================================================================================================================================================================]
[ 100% ]</div>
</div>
<div>
<div>2015-03-26 10:51:38 -
Calculating consequences</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'2853',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'HYPERTENSION, ESSENTIAL,
SUSCEPTIBILITY TO'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'20384',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'Susceptibility_to_progression_to_renal_failure_in_IgA_nephropathy'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'20369',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'Preeclampsia,_susceptibility_to'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'26451',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'HYPERTENSION,_ESSENTIAL,_SUSCEPTIBILITY_TO'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'1',</div>
<div> 'name' =>
'HGMD_MUTATION',</div>
<div>
'description' => 'Annotated
by HGMD but no phenotype
description is publicly
available'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'6522',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'COSMIC:tumour_site:large_intestine'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'6529',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'COSMIC:tumour_site:breast'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'2853',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'HYPERTENSION, ESSENTIAL,
SUSCEPTIBILITY TO'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'20384',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'Susceptibility_to_progression_to_renal_failure_in_IgA_nephropathy'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'20369',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'Preeclampsia,_susceptibility_to'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'26451',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'HYPERTENSION,_ESSENTIAL,_SUSCEPTIBILITY_TO'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'1',</div>
<div> 'name' =>
'HGMD_MUTATION',</div>
<div>
'description' => 'Annotated
by HGMD but no phenotype
description is publicly
available'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'6522',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'COSMIC:tumour_site:large_intestine'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div> 'adaptor'
=>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div> 'dbID' =>
'6529',</div>
<div> 'name' =>
undef,</div>
<div>
'description' =>
'COSMIC:tumour_site:breast'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>2015-03-26 10:51:38 -
Processed 1 total variants (1
vars/sec, 1 vars/sec total)</div>
<div>2015-03-26 10:51:38 - Wrote
stats summary to
variant_effect_output.txt_summary.html</div>
<div>2015-03-26 10:51:38 -
Finished!</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 26 March
2015 at 10:43, Guillermo Marco
Puche <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div text="#000066"
bgcolor="#FFFFFF"> Hello Will,<br>
<br>
I already had enabled
"check_existing" on my VEP
config template, however I
followed your advice and
updated code to force in the
new() method with your code.<br>
I'm still getting no prints of
line 64:<br>
<span><br>
print</span><span> Dumper(</span><span>$pf</span><span>-></span><span>phenotype());<br>
</span><br>
Are you getting any output
printed? As I said I get no
errors but nothing is printed
neither. This data dumper
should be printing result of
phenotype() method call.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<br>
<div>On 26/03/15 11:05,
Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">I think
perhaps you haven't
enabled
--check_existing; this
is required for
$vf->{existing} to
get populated.<br>
<div><br>
</div>
<div>You can force it
on in the new()
method of your
plugin:</div>
<div><br>
</div>
<div>$self->{config}->{check_existing}
= 1;</div>
<div><br>
</div>
<div>It then works for
me on release/75 and
release/79.</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div
class="gmail_quote">On
25 March 2015 at
17:35, Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0
0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div
text="#000066"
bgcolor="#FFFFFF">
Hello Will,<br>
<br>
With your
explanations I'm
trying to call
phenotype (as
you said I was
accessing the
hashref
directly).<br>
I'm using input
set you linked.
However my local
Ensembl
installation is
v75.<br>
<br>
This is the code
of the plugin:<br>
<a
moz-do-not-send="true"
href="https://github.com/guillermomarco/vep/blob/master/Clinvar.pm"
target="_blank">https://github.com/guillermomarco/vep/blob/master/Clinvar.pm</a><br>
<br>
I'm getting
absolutelty no
info nor errors.
I've no idea if
this is an issue
with my
database/API
version or with
the plugin code
itself.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<br>
<div>On
16/03/15
17:50, Will
McLaren wrote:<br>
</div>
<blockquote
type="cite">
<div dir="ltr">The
"is_significant"
field is an
internal flag
that doesn't
necessarily
have the
meaning you
expect; it is
used to
distinguish
between
genuine
reported
associations
and e.g.
non-significant
associations
reported from
genome-wide
studies.
<div><br>
</div>
<div>You
should not see
undef for
phenotype; I
suspect you
are accessing
the hashref
directly
($pf->{phenotype})
rather than
making the
method call
($pf->phenotype()).</div>
<div><br>
</div>
<div>You could
try <a
moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/release-79/variation/vcf/homo_sapiens/Homo_sapiens_clinically_associated.vcf.gz"
target="_blank">ftp://ftp.ensembl.org/pub/release-79/variation/vcf/homo_sapiens/Homo_sapiens_clinically_associated.vcf.gz</a>
as a test
input set.</div>
<div><br>
</div>
<div>Will</div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
16 March 2015
at 16:39,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote">
<div> Hi Will,<br>
<br>
Thank you for
your quick
response! Very
clarifying.<br>
<br>
I guess that
the way to
retrieve
ClinVar data I
posted is
correct. With
my test
dataset I've
only seen
"is_significant"
values of "1"
and undef
'phenotype'
values. I
think I need a
synthetic vcf
with ClinVar
annotation
variants to
very that the
plugin is
working.<br>
<br>
I've been
looking on
Ensembl
website for a
test dataset.
I think you
don't provide
any right?
Correct me if
I'm wrong.<br>
<br>
Thanks!<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<div>On
16/03/15
16:16, Will
McLaren wrote:<br>
</div>
<blockquote
type="cite">
<div dir="ltr">Hi
Guillermo,
<div><br>
</div>
<div>To get
the rest of
that data in
the table you
need to access
the additional
attributes of
the
PhenotypeFeature
object,
something
like:</div>
<div><br>
</div>
<div>my $attr
=
$pfs->[0]->get_all_attributes;<br>
</div>
<div>print
"$_:".$attr->{$_}."\t"
for keys
%$attr;</div>
<div>print
"\n;</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
<div><br>
</div>
<div>More
info: the
reason these
data are
stored as
attributes is
due to the
diverse data
sources and
types that we
import into
our phenotype
schema; to
create a
database
column and
corresponding
API method for
each data type
(p-value,
review status,
risk allele,
external ID
etc etc) would
be cumbersome
and
inefficient.
To this end we
provide a few
methods that
shortcut the
attribute
approach for
the most
common data
types;
everything
else must be
accessed
through the
attributes
method. This
is a common
theme across
the Ensembl
API.</div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
13 March 2015
at 12:03,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote">
<div> Hi,<br>
<br>
I'm trying to
retrieve
ClinVar
information
with the code
example you
provided.<span><br>
<br>
my $self =
shift;<br>
my $tva =
shift;<br>
my $vf =
$tva->variation_feature;<br>
my $pfa =
$self->{config}->{reg}->get_adaptor('human','variation','phenotypefeature');<br>
<br>
foreach my
$known_var(@{$vf->{existing}
|| []}) {<br>
foreach my
$pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})})
{<br>
</span>
if
($pf->{'source'}
eq
"dbSNP_ClinVar"){<br>
print
"$pf->{'source'}\t$pf->{'external_id'}\t$pf->{'is_significant'}\t$pf->{'phenotype'}\n",
;<br>
}<br>
}<br>
}<br>
<br>
As you can see
I'm
"filtering"
the results to
only output
phenotype
feature when
source is
dbSNP_ClinVar.
I don't know
why but I
guess
filtering
should be done
when doing the
"fetch_all".<br>
<br>
On the other
hand I'm
trying to
retrieve
Disease,
Source and
Clinical
Significance
from this
example table:
<a
moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;r=8:19955518-19956518;v=rs268;vdb=variation;vf=266"
target="_blank">http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;r=8:19955518-19956518;v=rs268;vdb=variation;vf=266</a><br>
<br>
I think I'm
doing
something
wrong I got
totally lost
in
Phenotypefeature.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<div>On
02/03/15
16:05, Will
McLaren wrote:<br>
</div>
<blockquote
type="cite">
<div dir="ltr">If
you enable the
--check_existing
flag when you
run the VEP,
you'll be able
to see any
known
co-located
variants
attached to
the
VariationFeature
object in your
plugin:
<div><br>
</div>
<div>sub run {</div>
my $self =
shift;
<div> my $tva
= shift;</div>
<div> my $vf
=
$tva->variation_feature;</div>
<div><br>
</div>
<div> foreach
my
$known_var(@{$vf->{existing}
|| []}) {</div>
<div> # do
stuff</div>
<div> }</div>
<div>}</div>
<div><br>
</div>
<div>The
$known_var is
not an API
object but a
simple hashref
with a number
of fields;
you're
probably
interested in
$known_var->{clin_sig}</div>
<div><br>
</div>
<div>However,
as I
mentioned,
this is the
only data that
is stored in
the cache. To
access the
rating and the
specific
disease
association,
you'll need to
make calls to
the database
by getting an
adaptor,
something
like:</div>
<div><br>
</div>
<div>
<div>sub run {</div>
<div> my
$self = shift;</div>
<div> my $tva
= shift;</div>
<div> my $vf
=
$tva->variation_feature;</div>
<div> my $pfa
=
$self->{config}->{reg}->get_adaptor('human','variation','phenotypefeature');</div>
<div><br>
</div>
<div> foreach
my
$known_var(@{$vf->{existing}
|| []}) {</div>
<div>
foreach my
$pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})})
{</div>
<div> #
do stuff</div>
<div> }</div>
<div> }</div>
<div>}</div>
</div>
<div><br>
</div>
<div>Be aware
that this will
access the
database, so
unless you
have a local
copy please
don't run this
sort of code
on genome-wide
VCFs using our
public DB
server.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
2 March 2015
at 14:47,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote">
<div> Hi Will,<br>
<br>
Indeed I'm
looking to
retrieve this
information
from VEP
plugin.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<div>On
02/03/15
15:25, Will
McLaren wrote:<br>
</div>
<blockquote
type="cite">
<div dir="ltr">Hi
Guillermo,
<div><br>
</div>
<div>The
detailed
ClinVar
information is
stored against
PhenotypeFeature
objects (each
SNP/disease
pairing gets
its own entry
in ClinVar,
e.g. <a
moz-do-not-send="true"
href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2"
target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2</a>, <a
moz-do-not-send="true"
href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/"
target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/</a>, <a
moz-do-not-send="true"
href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/"
target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/</a>
for rs699).</div>
<div><br>
</div>
<div>The
rating (and
indeed the
clinical
significance)
is stored as
an attribute
on the
PhenotypeFeature
object; you
can retrieve
this with the
get_all_attributes()
method.</div>
<div><br>
</div>
<div>See <a
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html"
target="_blank">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html</a>
and <a
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype"
target="_blank">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype</a>
for more info.</div>
<div><br>
</div>
<div><span>Bio::EnsEMBL::Variation::</span><span>Utils::VEP::get_clin_sig()
is an internal
method that
you should not
use.</span></div>
<div><span><br>
</span></div>
<div><span>The
VEP cache
contains the
list of
clinical
significance
states for
each variant,
but neither
the disease
association or
the rating. If
you want help
getting access
to this data
via a plugin,
let me know as
it's a little
more involved
than the API
methods above
(though it is
faster as no
database
access is
required).</span><br>
</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will
McLaren</div>
<div>Ensembl
Variation</div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
2 March 2015
at 14:06,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote">
<div> Dear
devs,<br>
<br>
I'm looking
forward to
retrieve
ClinVar
information
and add it to
VEP
annotation.
From my
understanding
I should be
able to
retrieve
"Clinical
significance"
and "ClinVar
Rating".<br>
<br>
I've been
looking the
Varation API,
and I'm
confused. I
guess for
significance I
should use
Bio::EnsEMBL::Variation::Utils::VEP::get_clin_sig()
or
Bio::EnsEMBL::Variation::VariationFeature::get_all_clinical_significance_states().<br>
<br>
What about
ClinVar
rating? Is it
possible to
retrieve it
from API?<br>
<br>
Thanks!<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<br>
</div>
<br>
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