FASTA class errors

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FASTA class errors

Vallejos, Andrew

I tried integrating a FASTA class source:

 

 

    <source name="rat-chromosome-fasta" type="fasta">

                        <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>

                        <property name="fasta.attribute" value="primaryIdentifier"/>

                        <property name="fasta.synonymSource" value="RGD"/>

                        <property name="fasta.seqDataSourceName" value="Rat Genome Sequencing Consortium"/>

                        <property name="fasta.dataSetTitle" value="Rat chromosome sequence"/>

                        <property name="fasta.taxonId" value="10116"/>

                        <property name="fasta.includes" value="*.fasta" />

                        <property name="src.data.dir" location="/usr/local/ratmine_src_data/genome/fasta"/>

    </source>

 

And I am getting errors: cannot find symbol MRNA.  These errors are being thrown from files located in bio/sources/fasta/main/src/org/Intermine/bio/dataconversion/.

 

So do I just need to add this class to the model definition?

 

-Andrew

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]

 


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Re: FASTA class errors

Julie Sullivan
Yes, exactly.  mRNA used to be in the core model, but was removed.

> I tried integrating a FASTA class source:
>
>
>
>
>
>     <source name="rat-chromosome-fasta" type="fasta">
>
>                         <property name="fasta.className"
> value="org.intermine.model.bio.Chromosome"/>
>
>                         <property name="fasta.attribute"
> value="primaryIdentifier"/>
>
>                         <property name="fasta.synonymSource"
> value="RGD"/>
>
>                         <property name="fasta.seqDataSourceName"
> value="Rat Genome Sequencing Consortium"/>
>
>                         <property name="fasta.dataSetTitle" value="Rat
> chromosome sequence"/>
>
>                         <property name="fasta.taxonId" value="10116"/>
>
>                         <property name="fasta.includes" value="*.fasta"
> />
>
>                         <property name="src.data.dir"
> location="/usr/local/ratmine_src_data/genome/fasta"/>
>
>     </source>
>
>
>
> And I am getting errors: cannot find symbol MRNA.  These errors are
> being thrown from files located in
> bio/sources/fasta/main/src/org/Intermine/bio/dataconversion/.
>
>
>
> So do I just need to add this class to the model definition?
>
>
>
> -Andrew
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>



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