[ensembl-dev] VEP script runtime errors

[Will McLaren]

Hi Hardip,

My fix for this was simply to replace the line:


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

which just means that MOTIF_SCORE_DELTA won't get printed out if it is
not defined.

Will

On 26 January 2012 21:52, Hardip Patel <hardip.patel at anu.edu.au> wrote:
> 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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>>
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