Export

Default exporters in bio project

• tab/csv - tab or comma separated
• GFF3
• FASTA
• BED
• Galaxy - exports data in tab or BED format to Galaxy server

Appears on these pages:

• Query results page
• List analysis page
• Genomic Region Search results page

Create a custom exporter

You can add additional export options to your InterMine by creating a custom exporter.

1. Write Java classes to handle the data

   see BEDHttpExporter.java and BEDExporter.java

2. Add the class to your webconfig-model.xml file:

   <tableExportConfig id="bed" className="org.intermine.bio.web.export.BEDHttpExporter"/>

3. Update Struts config

   # struts-config-model.xml

   <action path="/bedExportAction" name="bedExportForm" type="org.intermine.web.struts.TableExportAction" parameter="method"/>

   # tiles-defs-model.xml

   <definition name="bedExportOptions.tile" path="/model/bedExportOptions.jsp" controllerUrl="/initSequenceFeatureExportOptions.do" />

   # struts-config-model-form.xml

   <form-bean name="bedExportForm" type="org.intermine.bio.web.struts.BEDExportForm"/>

Customisation

By default, SequenceFeature and Protein can be exported in FASTA format

fasta.export.classes = SequenceFeature,Protein

Exporter description

exporter.galaxy.description = Export to Galaxy

exporter.sequence.description=Export in FASTA format

exporter.gff3.description=Export in GFF3 format

exporter.bed.description=Export in BED format