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FASTA

Types of data loaded

features and their sequences. Will create a feature for each entry in a fasta file and set the sequence, the class of the feature to create is set for the whole file.

How to download the data

N/A - will parse any file in FASTA format

How to load the data into your mine

project XML example

<source name="flybase-dmel-gene-fasta" type="flybase-dmel-gene-fasta">
  <property name="flybase-dmel-gene-fasta.taxonId" value="7227"/>
  <property name="flybase-dmel-gene-fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila melanogaster"/>
  <property name="flybase-dmel-gene-fasta.dataSourceName" value="FlyBase"/>
  <property name="flybase-dmel-gene-fasta.className" value="org.intermine.model.bio.Gene"/>
  <property name="flybase-dmel-gene-fasta.classAttribute" value="primaryIdentifier"/>
  <property name="flybase-dmel-gene-fasta.includes" value="dmel-all-gene-*.fasta"/>
  <property name="src.data.dir" location="/DATA/flybase/fasta"/>
  <!-- add licence here -->
  <property name="flybase-dmel-gene-fasta.licence" value="https://creativecommons.org/licenses/by/4.0/"/>
</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
licence URL pointing to standard data licence for data updates DataSet.licence with value