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

[Will McLaren]

Obviously you could make that conditional too:

$DB::single = 1 if $test_seq == undef;


On 13 November 2013 10:53, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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