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<div class="moz-cite-prefix">Dear Will,<br>
<br>
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.<br>
<br>
perl variant_effect_predictor.pl -i example.vcf -o test.vcf
--genomes --species escherichia_coli<br>
<br>
-------------------- WARNING ----------------------<br>
MSG: escherichia_coli is not a valid species name (check DB and
API version)<br>
FILE: Bio/EnsEMBL/Registry.pm LINE: 1172<br>
CALLED BY: variant_effect_predictor.pl LINE: 653<br>
Ensembl API version = 67<br>
---------------------------------------------------<br>
<br>
-------------------- WARNING ----------------------<br>
MSG: escherichia_coli is not a valid species name (check DB and
API version)<br>
FILE: Bio/EnsEMBL/Registry.pm LINE: 1172<br>
CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 957<br>
Ensembl API version = 67<br>
---------------------------------------------------<br>
<br>
-------------------- EXCEPTION --------------------<br>
MSG: Can not find internal name for species 'escherichia_coli'<br>
STACK Bio::EnsEMBL::Registry::get_adaptor
/misc/ngseq/src/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:959<br>
STACK main::get_adaptors variant_effect_predictor.pl:1054<br>
STACK main::configure variant_effect_predictor.pl:766<br>
STACK toplevel variant_effect_predictor.pl:66<br>
Ensembl API version = 67<br>
---------------------------------------------------<br>
<br>
<br>
perl variant_effect_predictor.pl -i example.vcf -o test.vcf
--genomes --species arabidopsis_thaliana<br>
<br>
2012-09-19 12:50:31 - Starting...<br>
2012-09-19 12:50:31 - Detected format of input file as vcf<br>
2012-09-19 12:50:31 - Read 173 variants into buffer<br>
2012-09-19 12:50:31 - Analyzing chromosome 21<br>
2012-09-19 12:50:31 - Reading transcript data from cache and/or
database<br>
[=======================================================================================================================================================================================================]
[ 100% ]<br>
2012-09-19 12:50:37 - Retrieved 0 transcripts (0 mem, 0 cached,
0 DB, 0 duplicates)<br>
2012-09-19 12:50:38 - Analyzing variants<br>
[=======================================================================================================================================================================================================]
[ 100% ]<br>
2012-09-19 12:50:38 - Calculating and writing output<br>
[=======================================================================================================================================================================================================]
[ 100% ]<br>
2012-09-19 12:50:38 - Analyzing chromosome 22<br>
2012-09-19 12:50:38 - Reading transcript data from cache and/or
database<br>
[=======================================================================================================================================================================================================]
[ 100% ]<br>
2012-09-19 12:51:10 - Retrieved 0 transcripts (0 mem, 0 cached,
0 DB, 0 duplicates)<br>
2012-09-19 12:51:11 - Analyzing variants<br>
[=======================================================================================================================================================================================================]
[ 100% ]<br>
2012-09-19 12:51:11 - Calculating and writing output<br>
[=======================================================================================================================================================================================================]
[ 100% ]<br>
2012-09-19 12:51:11 - Processed 173 total variants<br>
2012-09-19 12:51:11 - Finished!<br>
<br>
<br>
On 9/19/2012 12:45 PM, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<pre>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 <a class="moz-txt-link-rfc2396E" href="mailto:Weihong.Qi@fgcz.ethz.ch" target="_blank"><Weihong.Qi@fgcz.ethz.ch></a> wrote:
</pre>
<blockquote type="cite">
<pre>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: <a class="moz-txt-link-abbreviated" href="mailto:weihong.qi@fgcz.ETHZ.ch" target="_blank">weihong.qi@fgcz.ETHZ.ch</a>
Web: <a class="moz-txt-link-freetext" href="http://www.fgcz.ch" target="_blank">http://www.fgcz.ch</a>
_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
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Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<pre>_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
List admin (including subscribe/unsubscribe): <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
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: <a class="moz-txt-link-abbreviated" href="mailto:weihong.qi@fgcz.ETHZ.ch" target="_blank">weihong.qi@fgcz.ETHZ.ch</a>
Web: <a class="moz-txt-link-freetext" href="http://www.fgcz.ch" target="_blank">http://www.fgcz.ch</a>
</pre>
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