def load_odict(fname):
def ogroups_to_odict_list(ogroups):
orthdict = dict([(p1,[p2 for p2 in og[1]]) for og in ogroups for
p1 in og[0]])
return orthdict
odict = ogroups_to_odict_list(orth.load_ogroups('','',fname=fname))
return odict
def load_paralogs(sp_base, sp_other, ogroup_max, other_ogroup_max):
"""
Get all pairwise base species paralogs from sharing orthogroups in the
inParanoid orthology files between the base and other species.
"""
ogs = orth.load_ogroups(sp_base, sp_other)
use_ogs = []
if ogroup_max:
for og_base, og_other in ogs:
if (len(og_base) <= ogroup_max
and (other_ogroup_max is None
or len(og_other) <= other_ogroup_max)):
use_ogs.append(og_base)
else:
use_ogs = ut.i0(base_ogs)
base_paralogs = pu.groups_to_pairs(use_ogs)
return base_paralogs
