[ensembl-dev] Prediction of consequence type for novel variants

[Will McLaren]

Hi Sung,

The coordinates would be the same regardless of the strand.

Start is _always_ 1 greater than end for an insertion, regardless of
strand or the size of the insertion.

Will

On 14 December 2010 14:58, Sung Gong <sung at bio.cc> wrote:
> Hi Will,
>
> One more question about start/end positions in case of indels.
>
> In the API document
> (http://www.ensembl.org/info/docs/Pdoc/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeature.html),
> it says:
>    # Variation feature representing a 2bp insertion
>    $vf = Bio::EnsEMBL::Variation::VariationFeature->new
>       (-start   => 1522,
>        -end     => 1521, # end = start-1 for insert
>        -strand  => -1,
>        -slice   => $slice,
>        -allele_string => '-/AA',
>        -variation_name => 'rs12111',
>        -map_weight  => 1,
>        -variation => $v2);
>
> The example above is only for -1 strand?
> How can I generalise to set -start and -end?
>
> Cheers,
> Sung
>
> On 10 December 2010 11:41, Will McLaren <wm2 at ebi.ac.uk> wrote:
>> Hi Sung
>>
>> The codons() method will work; it returns the codon something like:
>>
>> aGa/aCa
>>
>> where the base changed is in capital letters.
>>
>> Will
>>
>> On 10 December 2010 11:26, Sung Gong <sung at bio.cc> wrote:
>>> Hi Will,
>>>
>>> Thanks for the paper. I appreciate your work.
>>>
>>> Before aware of your script, I used to get the corresponding codon and
>>> the position (0, 1 or 2) where a single DNA variant occur using the
>>> core API.
>>> Any work-around for this?
>>>
>>> I found a 'codons' method from 'TranscriptVariation', but it is a
>>> method of ConsequenceType?
>>>
>>> Thought better to ask you before going further.
>>>
>>> Cheers,
>>> Sung
>>>
>>> On 9 December 2010 14:02, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>>> Hi Sung,
>>>>
>>>> There is a publication referring to the system, but it does not go
>>>> into great detail on the internal workings:
>>>>
>>>> http://bioinformatics.oxfordjournals.org/content/26/16/2069.abstract
>>>>
>>>> Here's an approximate flow of what happens in the API. The vast
>>>> majority of the code used is in the Core module
>>>> Bio::EnsEMBL::Utils::TranscriptAlleles.pm, mainly the methods
>>>> type_variation() and apply_aa_change():
>>>>
>>>> - find overlapping transcripts (using $vf->feature_Slice and
>>>> $slice->get_all_Transcripts), then for each transcript:
>>>>
>>>> - get transcript mapper and map variation's coordinates to cDNA, CDS and peptide
>>>>
>>>> - any variants that don't fall in the coding sequence are classified
>>>> here (e.g. INTRONIC, UPSTREAM) and the flow ends
>>>>
>>>> - if variation falls in exon (i.e. has defined CDS coordinates),
>>>> generate alternative codon(s) and resulting translation
>>>>
>>>> - compare translation to reference; classify as e.g.
>>>> SYNONYMOUS_CODING, NON_SYNONYMOUS_CODING
>>>>
>>>> We are currently working on an overhaul to this system which should
>>>> make it easier to comprehend by following the code.
>>>>
>>>> I would recommend trying to follow through the code in Perl's
>>>> debugger, using the "perl -d" option.
>>>>
>>>> Hope this helps
>>>>
>>>> Will McLaren
>>>> Ensembl Variation
>>>>
>>>> On 9 December 2010 13:19, Sung Gong <sung at bio.cc> wrote:
>>>>> Hi,
>>>>>
>>>>> I was thrilled to find that Ensembl API provides a nice script
>>>>> (ftp://ftp.ensembl.org/pub/misc-scripts/) which can predict the
>>>>> consequence types of novel variations.
>>>>> Also, good to see a good demonstration how to use the API for that purpose:
>>>>> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html
>>>>>
>>>>> Before realising the variation API can help predicting consequence
>>>>> type of novel variants, I used to use only core API to map the
>>>>> position of my variants to see whether they are within coding region,
>>>>> intron, exon and so on.
>>>>> Now, I wondered how the variation API works for that purpose - looked
>>>>> at the source code, but found it is somewhat overwhelming.
>>>>>
>>>>> Can anybody explain how the novel prediction works internally under the hood?
>>>>>
>>>>> Cheers,
>>>>> Sung
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list
>>>>> Dev at ensembl.org
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>
>>>>
>>>
>>
>