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

[Will McLaren]

Hi Duarte,

You can insert the line:

$DB::single = 1;

before the line you wish to break at in the code, and the debugger will
stop there.

Cheers

Will


On 13 November 2013 10:13, Duarte Molha <Duarte.Molha at ogt.com> wrote:

> 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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>
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