corwur / gfftoneo4j

Tools for importing GFF files to a Neo4J graph database

GFF Import to Neo4J

About

Utility to read GFF files into a Neo4J graph database.

The parser supports various GFF file formats and is very robust to variations, thanks to the use of parser combinator technology.

Creates the following graph database entities:

• Nodes of type gene, splicing, exon
• Relationships:
  • order between genes of a sequence in order of start position
  • transcribes between gene and its splicings
  • links between exons and introns in order of start position
  • mRNA between exons in a splicing
  • codes between exons and their splicing
  • in between introns and their splicing

Written in Scala

Dependencies

• SBT
• Neo4J

Development

Building

• Run sbt assembly
• This produces gfftoneo4j-assembly-0.1-SNAPSHOT.jar

Set up Neo4J

• Start Neo4j at some folder
• Browse to the shown Neo4J URL
• Use the default password 'neo4j' and change it to 'test'

Running

scala target/scala-2.11/gfftoneo4j-assembly-0.1-SNAPSHOT.jar 
	-f pathToFile 
	-t gffType 
	-u neo4jUrl

• Path to GFF file
• GFF file format (fpoae | gcf)
• Neo4J server address, eg bolt://127.0.0.1:7687