KOparse

A perl script to parse KOBAS 'annotate' output to tabular format.

KOBAS is a well known gene set enrichment tool, offering the capability to annotate provided sequences or IDs as well as conduct enrichment analysis. The annotation of transcripts or genes via homology comparison with for example Arabidopsis thaliana is a valueable tool to gain amongst others GO terms or Pathway IDs of previously unavailable annotations.

However, the format of the results after annotation is not very convenient, as it is not structured as a table. Therefore it is necessary to parse the achieved results of the annotate tool for potential use in downstream analysis.

'annotate_parser' is a perl script parsing the results of the 'Annotate' section to tabular format. Using the default settings on the KOBAS site, the columns of the formatted output table are in order: Query name, Gene id, Gene name, Entrez id, Pathway, GO and GO slim.

Usage

perl annotate_parser.pl -i inputfile -o outputfile

Arguments

Parameter	Description	Comment
-i	/path/to/input_file	comma separated if multiple
-o	/path/to/output_file	if not specified, output is send to the console
--tsv	output format	default: tab delimited
--csv	output format	default: tab delimited

Test

The 'test' folder contains a template file, generated with the 'annotate' tool from KOBAS using their provided test IDs.