[ensembl-dev] Feature slice issue

Sat Nov 22 01:37:04 GMT 2014

Hi all,

Just a heads up: the Ensembl API instructions have the old version of BioPerl (1.2.3) that I was using, hence why I was having this issue: http://www.ensembl.org/info/docs/api/api_installation.html ... Someone may want to update those.

Thanks!

-Konrad

On Fri, Nov 21, 2014 at 4:31 PM, Konrad Karczewski
<konradk at broadinstitute.org> wrote:

> Hi Will,
> Thanks! Looks like the BioPerl update actually was the culprit. All set now, thanks!
> On Fri, Nov 21, 2014 at 4:22 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>> Hi Konrad,
>> I can't recreate this issue, but my guess would be it's some combination of
>> incorrect assembly or FASTA file. Without knowing what setup you're using
>> it's hard for me to say exactly what.
>> If I run the following skeleton plugin:
>> package Skeleton;
>> use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
>> use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
>> sub run {
>>   my ($self, $tva) = @_;
>>   print STDERR "Sequence
>> ".$tva->variation_feature->feature_Slice->expand(1, 1)->seq."\n";
>>   return {};
>> }
>> 1;
>> I get the same results using 75, 76 and 77, using either --database or
>> --cache with a FASTA file:
>> 2014-11-21 09:19:35 - Read existing cache info
>> 2014-11-21 09:19:35 - Auto-detected FASTA file in cache directory
>> 2014-11-21 09:19:35 - Checking/creating FASTA index
>> 2014-11-21 09:19:35 - Loaded plugin: Skeleton
>> 2014-11-21 09:19:35 - Starting...
>> 2014-11-21 09:19:35 - Detected format of input file as vcf
>> 2014-11-21 09:19:35 - Read 1 variants into buffer
>> 2014-11-21 09:19:35 - Reading transcript data from cache and/or database
>> [==========]  [ 100% ]
>> 2014-11-21 09:19:35 - Retrieved 185 transcripts (0 mem, 185 cached, 0 DB, 0
>> duplicates)
>> 2014-11-21 09:19:35 - Analyzing chromosome 1
>> 2014-11-21 09:19:35 - Analyzing variants
>> [==========]  [ 100% ]
>> 2014-11-21 09:19:35 - Calculating consequences
>> Sequence GCA
>> Sequence GCA
>> ...etc...
>> If using a FASTA file, double check the assembly matches that of your
>> cache, and re-generate the index. There are also known issues with older
>> version of BioPerl re: the FASTA indexing - make sure that you are using an
>> up to date (>1.6) version of BioPerl.
>> Regards
>> Will McLaren
>> Ensembl Variation
>> On 20 November 2014 21:06, Konrad Karczewski <konradk at broadinstitute.org>
>> wrote:
>>> Hi dev team,
>>>
>>> I've run into a strange issue when comparing output from v75 and v77. I'm
>>> looking to get 1 base context around a variant, which I've gotten using:
>>>
>>> $transcript_variation_allele->variation_feature->feature_Slice->expand(1,
>>> 1)->seq;
>>>
>>> When running this on a synthetic variant:
>>>
>>> 1       12141   .       C       A,T,G   .       .
>>>
>>> I get the expected result in v75 (note that context 1 bp around the
>>> variant is GCA as such:
>>> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A12140-12142
>>> <http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:12140-12142>
>>> )
>>>
>>>
>>> CSQ=A|ENSG00000223972|ENST00000456328|Transcript|non_coding_exon_variant&nc_transcript_variant|273||||||||1|1/3|||||||1||YES|DDX11L1|HGNC||||processed_transcript||||ENST00000456328.2:n.273C>A|||||||||||GCA,T|ENSG00000223972|ENST00000456328|Transcript|non_coding_exon_variant&nc_transcript_variant|273||||||||2|1/3|||||||1||YES|DDX11L1|HGNC||||processed_transcript||||ENST00000456328.2:n.273C>T|||||||||||GCA,G|ENSG00000223972|ENST00000456328|Transcript|non_coding_exon_variant&nc_transcript_variant|273||||||||3|1/3|||||||1||YES|DDX11L1|HGNC||||processed_transcript||||ENST00000456328.2:n.273C>G|||||||||||GCA,A|ENSG00000223972|ENST00000450305|Transcript|intron_variant&nc_transcript_variant|||||||||1||1/5||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000450305.2:n.49-38C>A|||||||||||GCA,T|ENSG00000223972|ENST00000450305|Transcript|intron_variant&nc_transcript_variant|||||||||2||1/5||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000450305.2:n.49-38C>T|||||||||||GCA,G|ENSG00000223972|ENST00000450305|Transcript|intron_variant&nc_transcript_variant|||||||||3||1/5||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000450305.2:n.49-38C>G|||||||||||GCA,A|ENSG00000223972|ENST00000515242|Transcript|non_coding_exon_variant&nc_transcript_variant|270||||||||1|1/3|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000515242.2:n.270C>A|||||||||||GCA,T|ENSG00000223972|ENST00000515242|Transcript|non_coding_exon_variant&nc_transcript_variant|270||||||||2|1/3|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000515242.2:n.270C>T|||||||||||GCA,G|ENSG00000223972|ENST00000515242|Transcript|non_coding_exon_variant&nc_transcript_variant|270||||||||3|1/3|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000515242.2:n.270C>G|||||||||||GCA,A|ENSG00000223972|ENST00000518655|Transcript|non_coding_exon_variant&nc_transcript_variant|268||||||||1|1/4|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000518655.2:n.268C>A|||||||||||GCA,T|ENSG00000223972|ENST00000518655|Transcript|non_coding_exon_variant&nc_transcript_variant|268||||||||2|1/4|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000518655.2:n.268C>T|||||||||||GCA,G|ENSG00000223972|ENST00000518655|Transcript|non_coding_exon_variant&nc_transcript_variant|268||||||||3|1/4|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000518655.2:n.268C>G|||||||||||GCA
>>>
>>> but same command/code running under VEP v77, I get this:
>>>
>>>
>>> CSQ=A|ENSG00000223972|ENST00000456328|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|273||||||1||1|DDX11L1|HGNC||processed_transcript|YES||||||||1/3|||ENST00000456328.2:n.273G>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000456328|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|273||||||2||1|DDX11L1|HGNC||processed_transcript|YES||||||||1/3|||ENST00000456328.2:n.273G>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000456328|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|273||||||3||1|DDX11L1|HGNC||processed_transcript|YES||||||||1/3|||||||||||||||||||||||CTT,A|ENSG00000223972|ENST00000450305|Transcript|intron_variant&non_coding_transcript_variant|||||||1||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene||||||||||1/5||ENST00000450305.2:n.49-38C>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000450305|Transcript|intron_variant&non_coding_transcript_variant|||||||2||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene||||||||||1/5||ENST00000450305.2:n.49-38C>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000450305|Transcript|intron_variant&non_coding_transcript_variant|||||||3||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene||||||||||1/5||ENST00000450305.2:n.49-38C>G||||||||||||||||||||CTT,A|ENSG00000223972|ENST00000515242|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|270||||||1||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/3|||ENST00000515242.2:n.270G>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000515242|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|270||||||2||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/3|||ENST00000515242.2:n.270G>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000515242|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|270||||||3||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/3|||||||||||||||||||||||CTT,A|ENSG00000223972|ENST00000518655|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|268||||||1||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/4|||ENST00000518655.2:n.268G>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000518655|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|268||||||2||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/4|||ENST00000518655.2:n.268G>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000518655|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|268||||||3||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/4|||||||||||||||||||||||CTT
>>>
>>> Any ideas why this might be the case? Happy to send the plugin and command
>>> line prompts if that would be helpful.
>>>
>>> Thanks!
>>> -Konrad
>>>
>>>
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