[ensembl-dev] variant effect predictor on bacteria genomes

[Weihong Qi]

Dear Will,

Thanks for the information. I tried this ealier and got an error stated 
that escherichia coli is not a valid species name. I tried the same with 
arabidopsis thaliana and it worked. So I thought I need special settings 
for connecting to the ensembl Bacteria. Screen dumps are appended as 
reference.

perl variant_effect_predictor.pl -i example.vcf -o test.vcf --genomes 
--species escherichia_coli

-------------------- WARNING ----------------------
MSG: escherichia_coli is not a valid species name (check DB and API version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1172
CALLED BY: variant_effect_predictor.pl  LINE: 653
Ensembl API version = 67
---------------------------------------------------

-------------------- WARNING ----------------------
MSG: escherichia_coli is not a valid species name (check DB and API version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1172
CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 957
Ensembl API version = 67
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: Can not find internal name for species 'escherichia_coli'
STACK Bio::EnsEMBL::Registry::get_adaptor 
/misc/ngseq/src/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:959
STACK main::get_adaptors variant_effect_predictor.pl:1054
STACK main::configure variant_effect_predictor.pl:766
STACK toplevel variant_effect_predictor.pl:66
Ensembl API version = 67
---------------------------------------------------


perl variant_effect_predictor.pl -i example.vcf -o test.vcf --genomes 
--species arabidopsis_thaliana

2012-09-19 12:50:31 - Starting...
2012-09-19 12:50:31 - Detected format of input file as vcf
2012-09-19 12:50:31 - Read 173 variants into buffer
2012-09-19 12:50:31 - Analyzing chromosome 21
2012-09-19 12:50:31 - Reading transcript data from cache and/or database
[=======================================================================================================================================================================================================] 
[ 100% ]
2012-09-19 12:50:37 - Retrieved 0 transcripts (0 mem, 0 cached, 0 DB, 0 
duplicates)
2012-09-19 12:50:38 - Analyzing variants
[=======================================================================================================================================================================================================] 
[ 100% ]
2012-09-19 12:50:38 - Calculating and writing output
[=======================================================================================================================================================================================================] 
[ 100% ]
2012-09-19 12:50:38 - Analyzing chromosome 22
2012-09-19 12:50:38 - Reading transcript data from cache and/or database
[=======================================================================================================================================================================================================] 
[ 100% ]
2012-09-19 12:51:10 - Retrieved 0 transcripts (0 mem, 0 cached, 0 DB, 0 
duplicates)
2012-09-19 12:51:11 - Analyzing variants
[=======================================================================================================================================================================================================] 
[ 100% ]
2012-09-19 12:51:11 - Calculating and writing output
[=======================================================================================================================================================================================================] 
[ 100% ]
2012-09-19 12:51:11 - Processed 173 total variants
2012-09-19 12:51:11 - Finished!


On 9/19/2012 12:45 PM, Will McLaren wrote:
> Hello,
>
> Yes this is possible assuming you know the species name for the
> bacteria you wish to use.
>
> You can use the --genomes flag which is a shortcut that makes the
> script connect to the Ensembl Genomes public server:
>
> perl variant_effect_predictor.pl -i variants.vcf --genomes --species
> [species_name]
>
> Thanks
>
> Will McLaren
> Ensembl Variation
>
> On 19 September 2012 10:55, Weihong Qi<Weihong.Qi at fgcz.ethz.ch>  wrote:
>> Dear Ensembl developers,
>>
>> Can the variant effect predictor (perl script) connect to Ensembl Bacteria
>> genomes? If it does, what will the command line switches be?
>>
>> Thanks,
>>
>> Weihong
>>
>> --
>> Weihong Qi, PhD
>> Functional Genomics Center Zurich
>> Uni/ETH Zurich
>> Winterthurerstrasse 190 / Y32 H66
>> CH-8057 Zurich
>>
>> Phone (Fixed line office):  +41 44 635 3964
>> Phone (Mobile office): +41 44 635 3997
>> Fax:  +41 44 635 3922
>> E-mail:weihong.qi at fgcz.ETHZ.ch
>> Web:http://www.fgcz.ch
>>
>>
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-- 
Weihong Qi, PhD
Functional Genomics Center Zurich
Uni/ETH Zurich
Winterthurerstrasse 190 / Y32 H66
CH-8057 Zurich

Phone (Fixed line office):  +41 44 635 3964
Phone (Mobile office): +41 44 635 3997
Fax:  +41 44 635 3922
E-mail:weihong.qi at fgcz.ETHZ.ch
Web:http://www.fgcz.ch

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