Quick ruby script to parse GO Annotation files (from http://geneontology.org) in order to generate some basic stats on the annotations in the file.

Requirements: rubygems - so you can use Bio::Ruby Bio::Ruby - uses their Gene annotation file parsing method

Usage: ruby qwik-e-gostats.rb gene_association.rgd > rgd_outputfile.txt

This will read in the gene_association.rgd file, parse the file and output the results as a tab-delimited text file to rgd_outputfile.txt

The results look like this:

Unique gene products: 28841 Unique sources: 11 Total number of annotation rows: 244035 Total number of non-unique annotation rows: 3 Total number of unique annotation rows: 244032 EC BHF-UCL ENSEMBL HGNC IntAct InterPro MGI PINC RGD Reactome Roslin_Institute UniProtKB EXP 0 0 0 0 0 0 0 0 159 0 0 159 IDA 263 0 162 0 0 338 0 15640 0 0 1007 17410 IPI 71 0 20 480 0 20 0 1999 0 1 435 3026 IMP 78 0 8 0 0 28 0 4667 0 0 127 4908 IGI 5 0 0 0 0 22 0 31 0 0 2 60 IEP 16 0 11 0 0 0 0 5297 0 0 19 5343 ISS 29 0 358 0 0 0 0 18 0 0 4747 5152 ISO 0 0 0 0 0 0 0 72746 0 0 0 72746 ISA 0 0 0 0 0 0 0 0 0 0 0 0 ISM 0 0 0 0 0 0 0 0 0 0 0 0 IGC 0 0 0 0 0 0 0 0 0 0 0 0 RCA 0 0 0 0 0 0 0 5064 0 0 0 5064 TAS 16 0 20 0 0 0 11 3029 0 0 150 3226 NAS 3 0 3 0 0 0 0 572 0 0 190 768 IC 10 0 1 0 0 1 0 141 0 0 16 169 ND* 0 0 3 0 0 0 0 4553 0 0 68 4624 IEA 0 26901 0 0 57988 0 0 0 0 0 36491 121380 Total Annotations: 491 26901 586 480 57988 409 11 113757 159 1 43252
Unique Genes Annotated: 126 5107 148 273 22601 196 9 12484 70 1 13242
Total Manual Genes Annotated: 120 0 95 273 0 196 9 5813 70 1 604 Total Manual Annotations: 462 228 480 409 11 35929 159 1 2014

If you generate two files, one using an older annotation file, one for the current file, you can copy and paste these results into excel and then subtract the newer results from the older results to get what has changed between the two annotation files. Can be useful for generating reports, etc.