[ensembl-dev] VEP script runtime errors

[Hardip Patel]

HI Will

Thank you so much for swift response. I was also wondering if I did introduce a line in the code to check if the value is defined before formatting, would I need to use a pseudo-score if the value is not defined. Meaning

if ($mfva->motif_score_delta){
   $line->{Extra}->{MOTIF_SCORE_DELTA} = sprintf "%.3f", $mfva->motif_score_delta;
}else{
   $line->{Extra}->{MOTIF_SCORE_DELTA} = 0;
}


or

should I just have

if ($mfva->motif_score_delta){
   $line->{Extra}->{MOTIF_SCORE_DELTA} = sprintf "%.3f", $mfva->motif_score_delta;
}

and not bother about the else situation?


Your help is greatly appreciated.

Thanking you.

Kind regards


Hardip R. Patel, PhD
Post-doctoral Research Fellow

Genome Discovery Unit and RNA Biology Lab
Genome Biology Department
The John Curtin School of Medical Research
College of Medicine, Biology and Environment
The Australian National University
Building 131, Garran Road, ANU Campus, Acton - 0200, ACT, Australia
Email: hardip.patel at anu.edu.au, patelhardip at gmail.com
Phone Number: (+61) 0449 180 715




On 27/01/2012, at 12:57 AM, Will McLaren wrote:

> Hi Hardip,
> 
> Thanks for your help in pointing these out.
> 
> None of them are anything to be concerned about - the last one, while
> it may appear bad, is just trying to format a number that hasn't been
> defined (we just need to change the code to check if it is defined
> before we try to format it).
> 
> We'll have all of them fixed for the next release.
> 
> Please do let us know if you spot any more!
> 
> Thanks
> 
> Will McLaren
> Ensembl Variation
> 
> On 26 January 2012 12:00, Hardip Patel <hardip.patel at anu.edu.au> wrote:
>> Dear all
>> 
>> I am trying to run vep script using local database and cache using the
>> following command.
>> 
>> perl variant_effect_predictor.pl --output_file output.vep --species
>> homo_sapiens --host localhost --user user --password password --port 1111
>> --db_version 65 --format vcf --buffer 1000000000 --terms ensembl --canonical
>> --hgnc --cache --regulatory --protein --gene --condel b --polyphen b --sift
>> b --force_overwrite --input_file input.vcf -skip_db_check
>> 
>> 
>> However, there are few warning thrown. Could somebody please let me know if
>> these warnings are acceptable and will not affect the output in anyways?
>> 
>> First warning:
>> Use of qw(...) as parentheses is deprecated at
>> /home/depressed/variant_effect_predictor/variant_effect_predictor.pl line
>> 848.
>> 
>> I am guessing this is the result of using perl v14.2 and also guessing that
>> this should not have any serious consequence at this stage.
>> 
>> Second warning is as follows:
>> 2012-01-26 17:11:42 - Reading cached adaptor data
>> Use of uninitialized value in join or string at
>> /home/depressed/ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 3495.
>> 
>> Again guessing that this doesn't cascade into serious trouble while
>> reporting results of the script.
>> 
>> However I am more concerned about following warnings (I get multiple of
>> them).
>> 
>> Use of uninitialized value in sprintf at
>> /home/depressed/ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 932, <GEN0> line 315932.
>> 
>> Trying to debug the code indicated that vcf line responsible for these are
>> (examples only out of many)
>> 
>> chr1 57005269 . AACACA AACA 217 .
>> INDEL;DP=25;VDB=0.0292;AF1=0.5;AC1=1;DP4=9,5,4,6;MQ=50;FQ=217;PV4=0.41,0.00046,1,0.38
>> GT:PL:DP:SP:GQ 0/1:255,0,255:24:4:99
>> chr1 61542770 . GAGGGGAGAAGGGG GAGGGGAGAAGGGGAGAAGGGG 106 .
>> INDEL;DP=23;VDB=0.0337;AF1=0.5;AC1=1;DP4=1,9,3,6;MQ=41;FQ=109;PV4=0.3,1,0,1
>> GT:PL:DP:SP:GQ 0/1:144,0,245:19:5:99
>> 
>> Any help on this matter is greatly appreciated.
>> 
>> Thanking you.
>> 
>> Kind regards
>> 
>> 
>> Hardip R. Patel, PhD
>> Post-doctoral Research Fellow
>> 
>> Genome Discovery Unit and RNA Biology Lab
>> Genome Biology Department
>> The John Curtin School of Medical Research
>> College of Medicine, Biology and Environment
>> The Australian National University
>> Building 131, Garran Road, ANU Campus, Acton - 0200, ACT, Australia
>> Email: hardip.patel at anu.edu.au, patelhardip at gmail.com
>> Phone Number: (+61) 0449 180 715
>> 
>> 
>> 
>> 
>> 
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