[ensembl-dev] Warning message in from VariationFeature.pm
Duarte Molha
duartemolha at gmail.com
Thu Aug 1 09:49:29 BST 2013
Thanks Will
I should have checked that before asking :S
I'll redownload and check if the error is gone ... thanks
Duarte
=========================
Duarte Miguel Paulo Molha
http://about.me/duarte
=========================
On Thu, Aug 1, 2013 at 9:46 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
> 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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