Source

orange-bioinformatics / server_update / updateOMIM.py

Marko Toplak b9f3957 


Flashpoint 3a530b6 
Marko Toplak 921b378 
Marko Toplak 6e88615 
Marko Toplak b9f3957 


Marko Toplak 921b378 
Marko Toplak b9f3957 







Marko Toplak 921b378 
Marko Toplak b9f3957 
Marko Toplak 921b378 
Flashpoint 3a530b6 









##!interval=7
##!contact=ales.erjavec@fri.uni-lj.si


from common import *
from Orange.bio import obiOMIM

import os, sys

path = os.path.join(environ.buffer_dir, "tmp_OMIM")

try:
    os.mkdir(path)
except OSError:
    pass
filename = os.path.join(path, "morbidmap")
obiOMIM.OMIM.download_from_NCBI(filename)

sf_server.upload("OMIM", "morbidmap", filename, title="Online Mendelian Inheritance in Man (OMIM)",
                   tags=["genes", "diseases", "human", "OMIM" "#version:%i" % obiOMIM.OMIM.VERSION])
sf_server.unprotect("OMIM", "morbidmap")


"""
Orange server upload for OMIM morbidmap gene sets
"""
from Orange.bio.obiGeneSets import omimGeneSets, register

omim_sets_split = omimGeneSets().split_by_hierarchy()
for omim_sets in omim_sets_split:
    register(omim_sets, sf_server)