Re: [GUSDEV] LoadFastaSequences.pm

[Mark S. H. <mh...@ug...>]

Here is one example.

ga GUS::Supported::Plugin::LoadFastaSequences  \
--externalDatabaseName 'C. parvum ORF50' \
--externalDatabaseVersion '2006-01-24' \
--sequenceFile /home/mheiges/CparvumORF50.fsa \
--regexSourceId '^>([^\t]+)\t[^\t]+\t[^\t]+$' \
--regexSecondaryId '^>[^\t]+\t([^\t]+)\t[^\t]+$' \
--regexChromosome '^>[^\t]+\t[^\t]+\t([^\t]+)$' \
--tableName 'DoTS::TranslatedAASequence' \
--commit


  regexSecondaryId and regexChromosome are optional.


On Jun 12, 2006, at 8:18 PM, mro...@cs... wrote:

> Folks:
>
> I am trying to run the LoadFastaSequences.pm plugin to add a sequence.
>
> The results from running LoadFastaSequences.pm --help are not very  
> clear
> to me.
>
> According to the instructions only 3 attributes are required, but I  
> found
> that it is not so, Gus wants data for other attributes, I am up to  
> 7 so
> far and is asking for more.
>
> Does anybody have a detailed listing with examples, of how Gus  
> wants the
> attributes when running the LoadFastaSequences.pm plugin?
>
> Cheers,
> Michael Robinson
> Bioinformatics Research Group (BioRG)
> Florida International University
> Miami FL 33199
>
>
>
>
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