new section in config file: disease via orthology

This release adds configuration options to separate the main disease sentence from disease via orthology and to treat them the two as independent modules

modified orthology sentence

Orthology sentence now include the prefix 'several human orthologs' when some of the orthologs in the Alliance are excluded by the 'best' ortholog filter.

New report fields

Added report fields for orthology and expression data

fixed report files and orthology template

minor bug fixes on reports and orthology module

reports serialization and diff files

• fixed bugs with report objects serialization
• added script to diff report files

read ontobio empty label

fixed bug that was breaking code when empty ontobio ontology label were present. Switched to ontobio label function to read labels using option id_if_null=True

New data structures based on Ontobio + disease module

• This release uses completely new data structures based on Ontobio and it introduces the disease and orthology modules for the descriptions.
• Orthology is still limited to WormBase data for now.
• Improved reports with more stats

merged hotfix for uppercase qualifier bug

Fix bug described here: https://agr-jira.atlassian.net/browse/AGR-1017

First release based on goatools

This is the first release of genedescriptions.

Main features:

• based on goatools data structure to manage ontologies and annotations
• generates gene descriptions for GO data only