add class2 nanopubs to fantom5 script. more refactoring.
remove module setup. fixed broken save_to_file method.
Change chromosome url pattern.
refactored nanopub converter code to a new class.
pushed option parser in to a converter method.
Update gene disease example with the new nanopub schema.
code style clean up.
new script for converting concept profile matching results to nanopublications.
replace tabs with spaces, and remove unused requires.
Merge pull request #2 from zuotian/master

new converter script for concept profile matching results + code/style clean up