def de_novo(): Arguments = namedtuple('Arguments', ['db', 'min_sample_depth'], verbose=True) # user clicked the "submit" button if request.GET.get('submit', '').strip(): min_sample_depth = str(request.GET.get('min-depth', '').strip()) igv_links = request.GET.get('igv_links') args = Arguments(db=database, min_sample_depth=min_sample_depth) de_novo_factory = \ GeminiInheritanceModelFactory(args, model="de_novo") de_novo_factory.get_candidates() if len(min_sample_depth) == 0: row_iter = \ de_novo_tool.get_de_novo_candidates(gq.c) else: row_iter = \ de_novo_tool.get_de_novo_candidates(gq.c, int(min_sample_depth)) return template('de_novo.j2', dbfile=database, rows=row_iter, igv_links=igv_links) else: return template('de_novo.j2', dbfile=database)
def run(parser, args): if os.path.exists(args.db): de_novo_factory = \ GeminiInheritanceModelFactory(args, model="de_novo") de_novo_factory.get_candidates()
def run(parser, args): if os.path.exists(args.db): mendel_violation_factory = \ GeminiInheritanceModelFactory(args, model="mendel_violations") mendel_violation_factory.get_candidates()
def run(parser, args): if os.path.exists(args.db): auto_dominant_factory = \ GeminiInheritanceModelFactory(args, model="auto_dom") auto_dominant_factory.get_candidates()
def run(parser, args): if os.path.exists(args.db): factory = GeminiInheritanceModelFactory(args, model="mendel_violations") factory.get_candidates()
def run(parser, args): if os.path.exists(args.db): auto_recessive_factory = \ GeminiInheritanceModelFactory(args, model="auto_rec") auto_recessive_factory.get_candidates()