[ensembl-dev] Error msg in VEP using HGVS option

Duarte Molha Duarte.Molha at ogt.com
Wed Nov 13 10:13:05 GMT 2013


Dear Sarah

I am having some difficulty pinpointing what line is causing the error since not all variations cause the error so  breaking at every single pass on that line is time consuming
Can you let me know of the best way of debugging the script in order to find that out?

Basically I want to run VEP and break the script at line 1220

/ensembl_API_folder/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm 

Where $test_seq is undefined

I tried running VEP in debug mode and do :

b /ensembl_API_folder/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm:1220 $test_seq == undef

Is this the way you would debug it?
Thanks for the help.

Duarte



-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Sarah Hunt
Sent: 11 November 2013 16:27
To: Ensembl developers list
Subject: Re: [ensembl-dev] Error msg in VEP using HGVS option

Hi Duarte,

A FASTA file is not a requirement for HGVS. Could you supply an example of a variant triggering this error message?

Thanks,

Sarah

On Mon, Nov 11, 2013 at 3:57 PM, Duarte Molha <Duarte.Molha at ogt.com> wrote:
> Dear Developers
>
>
>
> On the documentation, you indicate that you can use the option HGVS 
> but that it will need a valid connection to the database.
>
> However when I try to use it I get this error message:
>
>
>
> substr outside of string at
> /NGS_Tools/ensembl-latest/ensembl-variation/modules//Bio/EnsEMBL/Varia
> tion/TranscriptVariationAllele.pm
> line 1218.
>
> Use of uninitialized value $test_seq in string eq at 
> /NGS_Tools/ensembl-latest/ensembl-variation/modules//Bio/EnsEMBL/Varia
> tion/TranscriptVariationAllele.pm
> line 1220.
>
>
>
> If I supply a fasta file then I do not get this error. Is the FASTA 
> file always required for HGVS? From the documentation I got the 
> understanding that the fasta file was only required if operating in offline mode.
>
>
>
> Best regards
>
>
>
> Duarte Molha
>
>
>
>
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