GOgroup: A java jar executable to group Drosophila melanogaster genes
Description
GOgroup.jar is a executable java program used for clustering Drosophila melanogaster genes based on GeneOntology. The program takes as input a list of flybase gene ids to be clustered and list of GO ids based on which the clustering is to be done. For each GO id, a separate file is created with fly genes annotated to it or any of its child nodes.
Usage
at command prompt> java -jar GOgroup.jar <File_of_GOids> <File_of_FBgnids> <GO_OBO_file> <FBgn_GO_assoc_file>
<File_of_GOids> - A file containing list of GO ids for which drosophila genes need to be clustered. The format is as follows, with one entry per line
GO:0000101 GO:0007275
<File_of_FBgnids> - A file containing list of fly genes that need to be clustered. The format is as follows, with one entry per line
FBgn0000024 FBgn0000028 FBgn0000032
<GO_OBO_file> - Latest Gene Ontology database in obo format. You can download it from the Gene Ontology website. You should delete the following last 4 lines from the obo file.
[Typedef]
id: part_of
name: part of
is_transitive: true
<FBgn_GO_assoc_file> - The Flybase gene id to GO id mapping. You can download this from here.
For each GO id in the <File_of_GOids> , a separate file is created with a list of FBgns annotated to it or any of its child node. The files are named as the GOid with .txt extension. Eg; GO:0000101.txt