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Respect IMMU_SCOPE_WEIGHTS_DIR as first priority for determining ImmuScope weight directory #1462

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Respect IMMU_SCOPE_WEIGHTS_DIR as first priority for determining ImmuScope weight directory #1462

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15 changes: 6 additions & 9 deletions pvactools/lib/prediction_class.py
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Original file line number Diff line number Diff line change
Expand Up @@ -942,19 +942,16 @@ class NetMHCIIVersion:

class ImmuScope_IM(MHCII):
immuscope_score_col = 'ImmuScope_IM'
immuscope_weights_dir = '/opt/ImmuScope/weights'

def resolved_immuscope_weights_dir(self):
immu_scope_weights_dir = os.environ.get('IMMU_SCOPE_WEIGHTS_DIR')
xdg_data_home = os.environ.get('XDG_DATA_HOME')
if xdg_data_home:
user_dir = os.path.join(xdg_data_home, 'ImmuScope', 'weights')
if immu_scope_weights_dir:
return immu_scope_weights_dir
elif xdg_data_home:
return os.path.join(xdg_data_home, 'ImmuScope', 'weights')
else:
user_dir = os.path.join(os.path.expanduser('~/.local/share'), 'ImmuScope', 'weights')

if os.path.isdir(os.path.join(user_dir, 'IM')):
return user_dir

return self.immuscope_weights_dir
return os.path.join(os.path.expanduser('~/.local/share'), 'ImmuScope', 'weights')

def valid_allele_names(self):
"""Return allele names supported by ImmuScope.
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