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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:<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><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.<br>
<br>
<br>
<div class="moz-cite-prefix">On 26/03/15 12:57, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX1B92bnroY7kq0JZAKoF8F72cQCjBZoyF38xWGpZpnHKQ@mail.gmail.com"
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 class="h5"><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>
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