[ensembl-dev] Possible bug in VEP(v73)

[Will McLaren]

Hello,

Thank you for finding this issue, I have fixed the code on our CVS server -
if you re-download the VEP script you should not see this issue.

Regards

Will McLaren
Ensembl Variation


On 18 October 2013 17:46, saurabh gupta <saurabh at ganitlabs.in> wrote:

> Dear Fiona,
>
> Please do let me know if I am wrong.
>
> --
> Saurabh Gupta
> Ganit Labs, Bangalore
>
>
> On Fri, Oct 18, 2013 at 10:12 PM, Fiona Cunningham <fiona at ebi.ac.uk>wrote:
>
>> Dear Saurabh,
>>
>> Many thanks for taking the time to report this to us. We will take a look.
>>
>> Best regards,
>> Fiona
>>
>>
>> ---------------------------------------------------------------------------------------------------------------
>> Fiona Cunningham, Ensembl Coordinator, Ensembl Variation Project Leader.
>> European Bioinformatics Institute (EMBL-EBI)
>> European Molecular Biology Laboratory
>> Wellcome Trust Genome Campus
>> Hinxton,  CB10 1SD, UK
>> www.ensembl.org || www.lrg-sequence.org || t: +44 1223 494612
>>
>>
>> On 18 October 2013 07:22, saurabh gupta <saurabh at ganitlabs.in> wrote:
>> > Hi,
>> >
>> > I had downloaded the standalone version of VEP(v73) and was using it
>> > offline. When I tried using --hgvs with --offline I was getting an
>> error:
>> > "ERROR: Cannot generate HGVS coordinates in offline mode without a FASTA
>> > file (see --fasta)". However I had specified the --fasta option as well.
>> > After going through the code it seems the condition(line 954) is
>> checking if
>> > $config{fasta_db} is defined or not and throwing this error. In the code
>> > $config{fasta_db} is initialized at a later stage, so it throws an
>> error.
>> >
>> > I changed $config{fasta_db} to $config{fasta} on line 954(where the
>> > condition is checked) in variant_effect_predictor.pl and it worked.
>> >
>> > You guys might want to incorporate/modify this in the code.
>> >
>> > --
>> > Saurabh Gupta
>> > Ganit Labs, Bangalore
>> >
>> > _______________________________________________
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>>
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>
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