The easy way to do functional annotation of genomes and transcriptomes.
- Python 2.7
- MySql Database
- CairoSVG
- Cairo
- Tinycss
- Cssselect
- Pygal
- Pycha
easy_install CairoSVG tinycss cssselect pygal
Clone the git repository
git clone https://github.com/alejo0317/GeneOntology-Python.git
Edit the config.py file with your database settings (user, password, database)
Download the file idmapping.tab from ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb and use it to populate your local database to generate GeneOntology associations.
To populate the database with the file idmapping.tab use the script named mappingsToDB.py. This a populate example:
python2 mappingsToDb.py /path/to/idmapping.tab
You can use the scripts one by one or can use the full wrapper of all process.
Generates two files: a file containing relation between GO Terms and sequences, another file containing the tabbed counts of GO terms wanted.
Associantes Uniprot, Refseq, GI, accessions to GO identifiers using a mappings table.
Generates a Pie chart from a file with the GO counts.
We have include a set of files to test this scripts. You will find it on the folder test_data
A blast-generated-file with the querys and subjects (NR and Uniprot database has been used) A relation between Sequences and his associated GO terms. A relation between GO terms and his association with the Sequences. Ready to graph file. This file contain s the descriptions and relations bettwen the avaliable GO terms. Has been downloaded from http://purl.obolibrary.org/obo/go.obo A list of "2nd level" GO terms from the GO category Celullar Component (GO:0005575) A list of "2nd level" GO terms from the GO category Biological Process (GO:0008150) A list of "2nd level" GO terms from the GO category Mollecular Function (GO:0003674)