<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Hi Bhavana,</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">I’m unable to replicate this issue. I’ve run your code (slightly modified to dump out the results, exact code at the end of this mail), and this is the result I see:</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><div id="bloop_customfont" style="margin: 0px;">$VAR1 = [</div><div id="bloop_customfont" style="margin: 0px;"> 'ENSP00000352610.4:p.Ala307ThrfsTer41',</div><div id="bloop_customfont" style="margin: 0px;"> 'ENSP00000269305.4:p.Ala307ThrfsTer34',</div><div id="bloop_customfont" style="margin: 0px;"> 'ENSP00000398846.2:p.Ala307ThrfsTer32',</div><div id="bloop_customfont" style="margin: 0px;"> 'ENSP00000391127.2:p.Ala307ThrfsTer40',</div><div id="bloop_customfont" style="margin: 0px;"> 'ENSP00000391478.2:p.Ala307ThrfsTer34',</div><div id="bloop_customfont" style="margin: 0px;"> 'ENSP00000425104.1:p.Ala175ThrfsTer?'</div><div id="bloop_customfont" style="margin: 0px;">];</div><div id="bloop_customfont" style="margin: 0px;"><br></div><div id="bloop_customfont" style="margin: 0px;">Double check that your API (both ensembl and ensembl-variation) is up to date for release/89.</div><div id="bloop_customfont" style="margin: 0px;"><br></div><div id="bloop_customfont" style="margin: 0px;">Regards</div><div id="bloop_customfont" style="margin: 0px;"><br></div><div id="bloop_customfont" style="margin: 0px;">Will McLaren</div><div id="bloop_customfont" style="margin: 0px;">Ensembl Variation</div></div> <div><br></div><div><br></div><div>###</div><div>use Bio::EnsEMBL::Registry;</div><div><br></div><div>my $reg = 'Bio::EnsEMBL::Registry';</div><div><br></div><div>$reg->load_registry_from_db(-host => 'ensembldb.ensembl.org', -species => 'homo sapiens', -user => 'anonymous', -port => 3337, -db_version => 89);</div><div>my $sa = $reg->get_adaptor('human', 'core', 'slice');</div><div>my $vfa = $reg->get_adaptor('human', 'variation', 'VariationFeature');</div><div>my $slice = $sa->fetch_by_region('chromosome', 17);</div><div>my $vf = Bio::EnsEMBL::Variation::VariationFeature->new(-start => 7576915, -end => 7577019, -slice => $slice,</div><div>-allele_string => 'TGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACC/-', -strand => 1, -adaptor => $vfa);</div><div>my $cons = $vf->get_all_TranscriptVariations;</div><div>my @hgvsp = grep { defined } map { $_->hgvs_protein } map { @{$_->get_all_alternate_TranscriptVariationAlleles} } @$cons;</div><div><br></div><div>use Data::Dumper;</div><div>$Data::Dumper::Maxdepth = 3;</div><div>$Data::Dumper::Indent = 1;</div><div>print STDERR Dumper \@hgvsp;</div> <div id="bloop_sign_1499859739474519040" class="bloop_sign"></div> <br><p class="airmail_on">On 11 July 2017 at 15:24:39, Bhavana Harsha (<a href="mailto:bh4@sanger.ac.uk">bh4@sanger.ac.uk</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div></div><div>
<title></title>
I forgot to mention that these are GRCh37 coordinates.
<div class=""><br class=""></div>
<div class="">Bhavana<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">Begin forwarded message:</div>
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<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From:</b></span> <span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Bhavana Harsha <<a href="mailto:bh4@sanger.ac.uk" class="">bh4@sanger.ac.uk</a>><br class=""></span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject:</b></span> <span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Possible bug in variation API - result
different from VEP</b><br class=""></span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date:</b></span> <span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">11 July 2017 at 14:17:20 BST<br class=""></span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">To:</b></span> <span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:dev@ensembl.org" class="">dev@ensembl.org</a><br class=""></span></div>
<br class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hello,
<div class=""><br class=""></div>
<div class="">For the following variant</div>
<div class="">17 75769157577019
TGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACC/-+</div>
<div class=""><br class=""></div>
<div class="">the correct protein consequence for the transcript
ENST00000269305 should be </div>
<div class="">ENSP00000269305.4:p.Ala307ThrfsTer34</div>
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<div class="">As is confirmed by the VEP web interface, REST API
and the VEP perl script.</div>
<div class=""><br class=""></div>
<div class=""><br class=""></div>
<div class="">However, when I try to get this using the Variation
API, I get</div>
<div class="">ENSP00000269305.4:p.Ala307Thr</div>
<div class=""><br class=""></div>
<div class="">This is how I’m using the API:</div>
<div class=""><br class=""></div>
<div class=""><font face="Menlo" class="">$reg->load_registry_from_db(-host => '<a href="http://ensembldb.ensembl.org/" class="">ensembldb.ensembl.org</a>', -species => 'homo sapiens', -user
=> 'anonymous', -port => 3337);</font></div>
<div class=""><font face="Menlo" class="">my $sa =
$reg->get_adaptor(‘human’, 'core', 'slice');</font></div>
<div class=""><font face="Menlo" class="">my $vfa =
$reg->get_adaptor('human', 'variation',
'VariationFeature');</font></div>
<div class=""><font face="Menlo" class="">my $slice =
$sa->fetch_by_region(‘chromosome', 17);</font></div>
<div class=""><font face="Menlo" class="">my $vf =
Bio::EnsEMBL::Variation::VariationFeature->new(-start =>
7576915, -end => 7577019, -slice =>
$slice, </font></div>
<div class=""><font face="Menlo" class="">-allele_string =>
‘TGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACC/-‘, -strand
=> 1, -adaptor => $vfa); </font></div>
<div class=""><font face="Menlo" class="">my $cons =
$vf->get_all_TranscriptVariations;</font></div>
<div class=""><font face="Menlo" class="">my @hgvsp = grep {
defined } map { $_->hgvs_protein } map {
@{$_->get_all_alternate_TranscriptVariationAlleles} }
@$cons;</font></div>
<div class=""><br class=""></div>
<div class=""><br class=""></div>
<div class="">I’m using v89 for the API and the VEP script.</div>
<div class=""><br class=""></div>
<div class="">Is there something I’m doing wrong in my
script?</div>
<div class=""><br class=""></div>
<div class=""><br class=""></div>
<div class="">Cheers,</div>
<div class="">Bhavana</div>
<br class="">
<br class="">
<div class=""><br class="webkit-block-placeholder"></div>
<div class="">
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---------------------------------------------<br class="">
Bhavana Harsha<br class="">
Bioinformatician<br class="">
COSMIC<br class="">
Wellcome Trust Sanger Institute<br class="">
Hinxton, UK<br class="">
CB10 1SA<br class=""></div>
<div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div>
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<br class=""></div>
</div>
</blockquote>
</div>
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