[ensembl-dev] Warning message in from VariationFeature.pm
Will McLaren
wm2 at ebi.ac.uk
Thu Aug 1 09:46:19 BST 2013
Hi Duarte,
I think this is a bug I've already found and fixed - can you update your
ensembl-variation API and try again?
Here's the fix for reference:
http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?root=ensembl&r1=1.101.2.4&r2=1.101.2.5
Will
On 1 August 2013 09:33, Duarte Molha <duartemolha at gmail.com> wrote:
> I believe the main problem is that this Variation feature, for some reason
> does not have a splice attached to it : 'slice' => undef
>
> so the method to extract the slice and expand
>
>
> 471: my $slice = $self->feature_Slice->expand(
> 472: MAX_DISTANCE_FROM_TRANSCRIPT,
> 473: MAX_DISTANCE_FROM_TRANSCRIPT
> 474: );
>
> Fails.
>
> Anyone knows what might be causing this?
>
> Best regards
>
> Duarte
>
>
>
> =========================
> Duarte Miguel Paulo Molha
> http://about.me/duarte
> =========================
>
>
> On Wed, Jul 31, 2013 at 5:05 PM, Duarte Molha <duartemolha at gmail.com>wrote:
>
>> In an effort to understand better what might be causing this ... here is
>> a dumb of one such object causing the error message:
>>
>> the VCF line:
>> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
>> sample-01 sample-02 sample-03 sample-04 sample-05 sample-06
>> 1 I777437 I. IA IC I667.93 IPASS
>> IAC=1;AF=0.083;AN=12;BaseQRankSum=6.089;DP=487;Dels=0.00;FS=1.662;HRun=0;HaplotypeScore=0.9613;MQ=44.32;MQ0=49;MQRankSum=-1.435;QD=8.35;ReadPosRankSum=-1.520;SB=-247.14;set=variant2
>> IGT:AD:DP:GQ:PL I0/0:60,0:60:99:0,138,1819 I0/0:82,0:82:99:0,205,2614
>> I0/1:52,28:80:99:706,0,1290 I0/0:100,0:100:99:0,253,3074
>> I0/0:83,0:83:99:0,178,2360 I0/0:82,0:82:99:0,166,2135
>>
>> at line 471 of /Bio/EnsEMBL/Variation/VariationFeature.pm
>>
>> my object $self contains:
>>
>> 0 Bio::EnsEMBL::Variation::VariationFeature=HASH(0x57802b0)
>> '_line' =>
>> "1\cI777437\cI.\cIA\cIC\cI667.93\cIPASS\cIAC=1;AF=0.083;AN=12;BaseQRankSum=6.089;DP=487;Dels=0.00;FS=1.662;HRun=0;HaplotypeScore=0.9613;MQ=44.32;MQ0=49;MQRankSum=-1.435;QD=8.35;ReadPosRankSum=-1.520;SB=-247.14;set=variant2\cIGT:AD:DP:GQ:PL\cI0/0:60,0:60:99:0,138,1819\cI0/0:82,0:82:99:0,205,2614\cI0/1:52,28:80:99:706,0,1290\cI0/0:100,0:100:99:0,253,3074\cI0/0:83,0:83:99:0,178,2360\cI0/0:82,0:82:99:0,166,2135"
>> 'adaptor' =>
>> Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor=HASH(0x4b06030)
>> '_is_multispecies' => ''
>> 'db' => Bio::EnsEMBL::Variation::DBSQL::DBAdaptor=HASH(0x52b4f08)
>> '_dbc' => Bio::EnsEMBL::DBSQL::DBConnection=HASH(0x52b50d0)
>> '_dbname' => 'homo_sapiens_variation_72_37'
>> '_driver' => 'mysql'
>> '_host' => 'ensembldb.ensembl.org'
>> '_port' => 5306
>> '_query_count' => 4
>> '_timeout' => 0
>> '_username' => 'anonymous'
>> 'connected32406' => 1
>> 'db_handle32406' => DBI::db=HASH(0x51e5ee8)
>> empty hash
>> 'reconnect_when_lost' => 1
>> '_group' => 'variation'
>> '_is_multispecies' => ''
>> '_no_cache' => 1
>> '_species' => 'homo_sapiens'
>> '_species_id' => 1
>> 'dbc' => Bio::EnsEMBL::DBSQL::DBConnection=HASH(0x52b50d0)
>> -> REUSED_ADDRESS
>> 'species_id' => 1
>> 'allele_string' => 'A'
>> 'chr' => 1
>> 'end' => 777437
>> 'existing' => ARRAY(0x10861900)
>> empty array
>> 'genotype' => ARRAY(0x577ff80)
>> 0 'A'
>> 1 'A'
>> 'individual' => 'sample-01'
>> 'map_weight' => 1
>> 'non_variant' => 1
>> 'phased' => 1
>> 'slice' => undef
>> 'start' => 777437
>> 'strand' => 1
>> 'variation_name' => '1_777437_A'
>>
>>
>>
>>
>> =========================
>> Duarte Miguel Paulo Molha
>> http://about.me/duarte
>> =========================
>>
>>
>> On 31 July 2013 13:52, Duarte Molha <duartemolha at gmail.com> wrote:
>>
>>> Hi Devs
>>>
>>> I have been trying to run a VCF file by the variant annotation script
>>> and I've been getting a warning message that I have never before
>>> encountered..
>>>
>>> I was wondering if someone could let me know if it is something I am
>>> doing wrong…
>>>
>>> The message is :
>>>
>>> *Can't call method "expand" on an undefined value at
>>> <sic>/Bio/EnsEMBL/Variation/VariationFeature.pm line 471*
>>>
>>> **
>>>
>>> * *
>>>
>>> Here are the configuration options I am using:
>>>
>>>
>>>
>>> Configuration options:
>>>
>>> ###
>>>
>>> allow_non_variant 1
>>>
>>> cache 1
>>>
>>> canonical 1
>>>
>>> ccds 1
>>>
>>> check_alleles 1
>>>
>>> check_existing 1
>>>
>>> config vep_human.ini
>>>
>>> core_type core
>>>
>>> custom
>>> ./vep_additional_annotations/Somatic_variation_phenotypes.bed.gz,Somatic,bed,exact
>>> ./vep_additional_annotations/dbsnp135_ensembl_variation_phenotype.bed.gz,dbsnp135,bed,exact
>>>
>>> db_version 72
>>>
>>> dir /ReferenceData/vep_cache
>>>
>>> dir_cache /ReferenceData/vep_cache
>>>
>>> dir_plugins ./Plugins
>>>
>>> domains 1
>>>
>>> force_overwrite 1
>>>
>>> fork 5
>>>
>>> gmaf 1
>>>
>>> hgnc 1
>>>
>>> host ensembldb.ensembl.org
>>>
>>> individual all
>>>
>>> input_file All_BOTH_SNPINDELfilter_PASSED.vcf
>>>
>>> maf_1kg 1
>>>
>>> numbers 1
>>>
>>> output_file All_BOTH_SNPINDELfilter_PASSED.ann
>>>
>>> plugin
>>> OGT_NHBLI_MAF,/ReferenceData/NHLBI_EVS/NHLBI_OGT.gz
>>> OGT_selected_VCF_fields_output Blosum62 Carol OGT_Condel,b
>>> OGT_Grantham TSSDistance Downstream
>>>
>>> polyphen b
>>>
>>> port 5306
>>>
>>> protein 1
>>>
>>> regulatory 1
>>>
>>> sift b
>>>
>>> species homo_sapiens
>>>
>>> stats HASH(0x4370ad8)
>>>
>>> terms SO
>>>
>>> verbose 1
>>>
>>>
>>>
>>> I would be very grateful for your help.
>>>
>>> Duarte Molha
>>>
>>
>>
>
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