gff3tools

gff3tools is a Java library for converting EMBL flat files to GFF3 format. It uses sequencetools to read the flat file.

Compiling

To access the sequencetools library, create the gradle.properties file and add your private EBI gitlab token in the following format.

gitlab_private_token=<token>

Conversion Rules and Assumptions

Conversion rules and Assumptions are added to the code under // Rule: and // Assumption: comments for now.

Building the project

Checkout the project

• Clone the project

git clone https://github.com/EBIBioStudies/gff3tools.git

• Change dir

cd gff3tools

• Build the project

./gradlew clean build

The jar file will be found in /build/lib/gff3tools*.jar. You can use this jar to run the converter.

Usage

java -jar gff3tools-1.0.jar help

Defaults and conventions

• The conversion tool will identify file formats using the file extension. Only gff3 and ff are recognised file extensions
• The parameters -f (from) and -t (to) can be used to specify the file format if the extension is not recognised or if using std-in/std-out
• If not provided the parameter -t (to) will default to gff3

Converter

FF to GFF3 java -jar gff3tools-1.0.jar conversion OZ026791.ff OZ026791.gff3

GFF3 to FF java -jar gff3tools-1.0.jar conversion OZ026791.gff3 OZ026791.ff

Using unix pipes

The converter supports unix pipes, input and output using std-in and std-out.

From gff3 stdin to ff stdout

cat OZ026791.gff3 | java -jar gff3tools-1.0.jar conversion -f gff3 -t ff > OZ026791.ff