Re: [GUSDEV] Gusdev-gusdev Digest, Vol 1, Issue 797

[<mro...@cs...>]

Thank you very much.
It worked perfectly, I just adjusted the regular expressions to match my
data.


My data was a fasta data file and this was the adjustment:
--regexSourceId '>(\S+)\s'

Is there a place where I can obtain samples of how to run all Plugins?


Thanks again

Michael Robinson
Bioinformatics Research Group (BioRG)
Florida International University
Miami FL 33199



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>    1. LoadFastaSequences.pm (mro...@cs...)
>    2. Re: LoadFastaSequences.pm (Mark S. Heiges)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 12 Jun 2006 20:18:48 -0400 (EDT)
> From: mro...@cs...
> Subject: [GUSDEV] LoadFastaSequences.pm
> To: gus...@li...
> Message-ID: <196...@ww...>
> Content-Type: text/plain;charset=3Diso-8859-1
>
> Folks:
>
> I am trying to run the LoadFastaSequences.pm plugin to add a sequence.
>
> The results from running LoadFastaSequences.pm --help are not very clea=
r
> to me.
>
> According to the instructions only 3 attributes are required, but I fou=
nd
> 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 th=
e
> attributes when running the LoadFastaSequences.pm plugin?
>
> Cheers,
> Michael Robinson
> Bioinformatics Research Group (BioRG)
> Florida International University
> Miami FL 33199
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 12 Jun 2006 20:42:34 -0400
> From: "Mark S. Heiges" <mh...@ug...>
> Subject: Re: [GUSDEV] LoadFastaSequences.pm
> To: GUS-Dev gusdev-gusdev <gus...@li...>
> Message-ID: <1B6...@ug...>
> Content-Type: text/plain; charset=3DUS-ASCII; delsp=3Dyes; format=3Dflo=
wed
>
> 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
>>
>>
>>
>>
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
>
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> End of Gusdev-gusdev Digest, Vol 1, Issue 797
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