BioSources > fasta

The fasta source loads features and their sequences and will create a feature for each entry in a fasta file and set the sequence.

To configure a fasta source, add an entry to the project.xml file, like so:

    <!-- example from flymine/project.xml -->
    <source name="uniprot-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227 7237 6239 7165 7460 4932 9606 10090"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryAccession"/>
      <property name="fasta.dataSetTitle" value="UniProt data set"/>
      <property name="fasta.dataSourceName" value="UniProt"/>
      <property name="src.data.dir" location="/data/uniprot/current"/>
      <property name="fasta.includes" value="uniprot_sprot_varsplic.fasta"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.UniProtFastaLoaderTask"/>
    </source>

attribute	content	purpose
taxonId	space-delimited list of taxonIds	only features with the listed taxonIds will be loaded
className	fully-qualified class name	determines which feature will be loaded
classAttribute	identifier field from className	determines which field from the feature will be set
dataSetTitle	name of dataset	determines name of dataset object
dataSourceName	name of datasource	determines name of datasource object
src.data.dir	location of the fasta data file	these data will be loaded into the database
includes	name of data file	this data file will be loaded into the database
sequenceType	class name	type of sequence to be loaded
loaderClassName	name of Java file that will process the fasta files	only use if you have created a custom fasta loader

datasets and datasources

Proteins, genes, and chromsomes have a datasets collection. A dataset is set of results or data from a datasource. A dataset has a reference to a datasource, which is from which organisation the data came from.

See FlyMine's project.xml file for more examples.

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