[ensembl-dev] Error msg in VEP using HGVS option
Duarte Molha
Duarte.Molha at ogt.com
Wed Nov 13 12:26:02 GMT 2013
Hi Sarah and Will...
Here is one of the lines that produces the error:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample
6 32191658 . TAGCAGCAGCAGC TAGCAGCAGCAGCAGC,T,TAGCAGCAGC 16674.03 PASS AC=1,0,0;AF=0.333,0.167,0.250;AN=2;BaseQRankSum=5.772;DP=625;FS=7.430;HaplotypeScore=193.1707;MQ0=0;MQ=54.55;MQRankSum=-1.450;QD=26.68;ReadPosRankSum=1.084;SB=-6459.41;set=variant GT:AD:DP:GQ:PL 0/1:91,0,0,0:126:99:1559,0,2016,1848,2305,13600,1821,2144,5419,5130
Perhaps these types of INDELS should be included in tests before release? They are not very common I am sure but, I can tell you that they have been a pain to debug!
Thanks :)
Duarte
-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Duarte Molha
Sent: 13 November 2013 11:59
To: Ensembl developers list
Subject: Re: [ensembl-dev] Error msg in VEP using HGVS option
Thank you both Sarah and Will.
I believe that is probably what is causing the issue on line 1218.
I was able to stop the script at the problematic line... but I still am having an issue getting the input vcf line that is causing it.
The $self object contains a massive amount of data. How can I extract the input line from it?
In the meantime I'll checkout the latest code and see if that fixes it.
Best regards
Duarte
-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Sarah Hunt
Sent: 13 November 2013 11:31
To: Ensembl developers list
Subject: Re: [ensembl-dev] Error msg in VEP using HGVS option
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/V
>>> > aria
>>> > tion/TranscriptVariationAllele.pm
>>> > line 1218.
>>> >
>>> > Use of uninitialized value $test_seq in string eq at
>>> > /NGS_Tools/ensembl-latest/ensembl-variation/modules//Bio/EnsEMBL/V
>>> > aria
>>> > 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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