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

[Sarah Hunt]

Hi Duarte,

I've made a modification to branch 73 TranscriptVariationAllele.pm in
CVS. Long insertions at the start of transcripts could give rise to
the 'substr outside of string' error. Could you update your install
and see if this fixes the problem?


Thanks,

Sarah

On Wed, Nov 13, 2013 at 10:54 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
> 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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