Export¶
Default exporters in bio project
- tab/csv - tab or comma separated
- GFF3
- FASTA
- BED
- Galaxy - export 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.
Write Java classes to handle the data
see BEDHttpExporter.java and BEDExporter.java
Add the class to your webconfig-model.xml file:
<tableExportConfig id="bed" className="org.intermine.bio.web.export.BEDHttpExporter"/>
- 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 as 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