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Make alpha chain first #83

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149 changes: 77 additions & 72 deletions stcrpy/tcr_processing/TCR.py
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Original file line number Diff line number Diff line change
Expand Up @@ -157,13 +157,13 @@ def get_TCR_type(self):
"""
if hasattr(self, "tcr_type"):
return self.tcr_type
elif hasattr(self, "VB") and hasattr(self, "VA"):
elif hasattr(self, "VA") and hasattr(self, "VB"):
self.tcr_type = "abTCR"
return self.tcr_type
elif hasattr(self, "VD") and hasattr(self, "VG"):
elif hasattr(self, "VG") and hasattr(self, "VD"):
self.tcr_type = "gdTCR"
return self.tcr_type
elif hasattr(self, "VB") and hasattr(self, "VD"):
elif hasattr(self, "VD") and hasattr(self, "VB"):
self.tcr_type = "dbTCR"
return self.tcr_type

Expand Down Expand Up @@ -563,7 +563,7 @@ def __init__(self, c1, c2):
c2 (TCRchain): alpha or beta type TCR chain
"""

if c1.chain_type == "B":
if c1.chain_type == "A":
Entity.__init__(self, c1.id + c2.id)
else:
Entity.__init__(self, c2.id + c1.id)
Expand All @@ -572,9 +572,9 @@ def __init__(self, c1, c2):
self.level = "H"
self._add_domain(c1)
self._add_domain(c2)
self.child_list = sorted(
self.child_list, key=lambda x: x.chain_type, reverse=True
) # make sure that the list goes B->A or G->D
# make sure that the list goes A->B, D->B, or D->G
chain_ordering = {'A': 1, 'B': 2, 'D': 1, 'G': 2}
self.child_list = sorted(self.child_list, key=lambda x: chain_ordering[x.chain_type])
self.antigen = []
self.MHC = []
self.engineered = False
Expand All @@ -589,7 +589,7 @@ def __repr__(self):
Returns:
str: String representation of the abTCR objec
"""
return "<TCR %s%s beta=%s; alpha=%s>" % (self.VB, self.VA, self.VB, self.VA)
return f"<TCR {self.VA}{self.VB} alpha={self.VA}; beta={self.VB}>"

def _add_domain(self, chain):
"""
Expand All @@ -599,24 +599,15 @@ def _add_domain(self, chain):
Args:
chain (TCRchain): TCR chain whose domain is being added.
"""
if chain.chain_type == "B":
self.VB = chain.id
elif chain.chain_type == "A" or chain.chain_type == "D":
if chain.chain_type == "A" or chain.chain_type == "D":
self.VA = chain.id

elif chain.chain_type == "B":
self.VB = chain.id

# Add the chain as a child of this entity.
self.add(chain)

def get_VB(self):
"""
Retrieve the variable beta chain of the TCR

Returns:
TCRchain: VB chain
"""
if hasattr(self, "VB"):
return self.child_dict[self.VB]

def get_VA(self):
"""
Retrieve the variable alpha chain of the TCR
Expand All @@ -627,6 +618,16 @@ def get_VA(self):
if hasattr(self, "VA"):
return self.child_dict[self.VA]

def get_VB(self):
"""
Retrieve the variable beta chain of the TCR

Returns:
TCRchain: VB chain
"""
if hasattr(self, "VB"):
return self.child_dict[self.VB]

def get_domain_assignment(self):
"""
Retrieve the domain assignment of the TCR as a dict with variable domain type as key and chain ID as value.
Expand All @@ -637,10 +638,10 @@ def get_domain_assignment(self):
try:
return {"VA": self.VA, "VB": self.VB}
except AttributeError:
if hasattr(self, "VB"):
return {"VB": self.VB}
if hasattr(self, "VA"):
return {"VA": self.VA}
if hasattr(self, "VB"):
return {"VB": self.VB}
return None

def is_engineered(self):
Expand All @@ -653,8 +654,8 @@ def is_engineered(self):
if self.engineered:
return True
else:
vb, va = self.get_VB(), self.get_VA()
for var_domain in [vb, va]:
va, vb = self.get_VA(), self.get_VB()
for var_domain in [va, vb]:
if var_domain and var_domain.is_engineered():
self.engineered = True
return self.engineered
Expand All @@ -669,10 +670,10 @@ def get_fragments(self):
Yields:
Fragment: fragment of TCR chain.
"""
vb, va = self.get_VB(), self.get_VA()
va, vb = self.get_VA(), self.get_VB()

# If a variable domain exists
for var_domain in [vb, va]:
for var_domain in [va, vb]:
if var_domain:
for frag in var_domain.get_fragments():
yield frag
Expand All @@ -699,16 +700,16 @@ def standardise_chain_names(self) -> None:
new_id = []
new_child_dict = {}

if hasattr(self, 'VB'):
new_child_dict['E'] = self.child_dict[self.VB]
self.VB = 'E'
new_id.append('E')

if hasattr(self, 'VA'):
new_child_dict['D'] = self.child_dict[self.VA]
self.VA = 'D'
new_id.append('D')

if hasattr(self, 'VB'):
new_child_dict['E'] = self.child_dict[self.VB]
self.VB = 'E'
new_id.append('E')

with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonWarning)

Expand All @@ -732,7 +733,7 @@ class gdTCR(TCR):

def __init__(self, c1, c2):

if c1.chain_type == "D":
if c1.chain_type == "G":
Entity.__init__(self, c1.id + c2.id)
else:
Entity.__init__(self, c2.id + c1.id)
Expand All @@ -741,9 +742,9 @@ def __init__(self, c1, c2):
self.level = "H"
self._add_domain(c1)
self._add_domain(c2)
self.child_list = sorted(
self.child_list, key=lambda x: x.chain_type
) # make sure that the list goes B->A or D->G
# make sure that the list goes A->B, D->B, or D->G
chain_ordering = {'A': 1, 'B': 2, 'D': 1, 'G': 2}
self.child_list = sorted(self.child_list, key=lambda x: chain_ordering[x.chain_type])
self.antigen = []
self.MHC = []
self.engineered = False
Expand All @@ -752,41 +753,44 @@ def __init__(self, c1, c2):
self.visualise_interactions = self._create_interaction_visualiser()

def __repr__(self):
return "<TCR %s%s delta=%s; gamma=%s>" % (self.VD, self.VG, self.VD, self.VG)
return f"<TCR {self.VG}{self.VD} gamma={self.VG}; delta={self.VD}>"

def _add_domain(self, chain):
if chain.chain_type == "D":
self.VD = chain.id
elif chain.chain_type == "G":
if chain.chain_type == "G":
self.VG = chain.id

elif chain.chain_type == "D":
self.VD = chain.id

# Add the chain as a child of this entity.
self.add(chain)

def get_VD(self):
if hasattr(self, "VD"):
return self.child_dict[self.VD]

def get_VG(self):
if hasattr(self, "VG"):
return self.child_dict[self.VG]

def get_VD(self):
if hasattr(self, "VD"):
return self.child_dict[self.VD]

def get_domain_assignment(self):
try:
return {"VG": self.VG, "VD": self.VD}
except AttributeError:
if hasattr(self, "VD"):
return {"VD": self.VD}
if hasattr(self, "VG"):
return {"VG": self.VG}

if hasattr(self, "VD"):
return {"VD": self.VD}

return None

def is_engineered(self):
if self.engineered:
return True
else:
vd, vg = self.get_VD(), self.get_VG()
for var_domain in [vd, vg]:
vg, vd = self.get_VG(), self.get_VD()
for var_domain in [vg, vd]:
if var_domain and var_domain.is_engineered():
self.engineered = True
return self.engineered
Expand All @@ -795,7 +799,7 @@ def is_engineered(self):
return False

def get_fragments(self):
vd, vg = self.get_VD(), self.get_VG()
vg, vd = self.get_VG(), self.get_VD()

# If a variable domain exists
for var_domain in [vg, vd]:
Expand Down Expand Up @@ -858,7 +862,7 @@ class dbTCR(TCR):
def __init__(self, c1, c2):
super(TCR, self).__init__()

if c1.chain_type == "B":
if c1.chain_type == "D":
Entity.__init__(self, c1.id + c2.id)
else:
Entity.__init__(self, c2.id + c1.id)
Expand All @@ -867,9 +871,9 @@ def __init__(self, c1, c2):
self.level = "H"
self._add_domain(c1)
self._add_domain(c2)
self.child_list = sorted(
self.child_list, key=lambda x: x.chain_type, reverse=False
) # make sure that the list goes B->D
# make sure that the list goes A->B, D->B, or D->G
chain_ordering = {'A': 1, 'B': 2, 'D': 1, 'G': 2}
self.child_list = sorted(self.child_list, key=lambda x: chain_ordering[x.chain_type])
self.antigen = []
self.MHC = []
self.engineered = False
Expand All @@ -878,41 +882,42 @@ def __init__(self, c1, c2):
self.visualise_interactions = self._create_interaction_visualiser()

def __repr__(self):
return "<TCR %s%s beta=%s; delta=%s>" % (self.VB, self.VD, self.VB, self.VD)
return f"<TCR {self.VD}{self.VB} delta={self.VD}; beta={self.VB}>"

def _add_domain(self, chain):
if chain.chain_type == "B":
self.VB = chain.id
elif chain.chain_type == "D":
if chain.chain_type == "D":
self.VD = chain.id

elif chain.chain_type == "B":
self.VB = chain.id

# Add the chain as a child of this entity.
self.add(chain)

def get_VB(self):
if hasattr(self, "VB"):
return self.child_dict[self.VB]

def get_VD(self):
if hasattr(self, "VD"):
return self.child_dict[self.VD]

def get_VB(self):
if hasattr(self, "VB"):
return self.child_dict[self.VB]

def get_domain_assignment(self):
try:
return {"VD": self.VD, "VB": self.VB}
except AttributeError:
if hasattr(self, "VB"):
return {"VB": self.VB}
if hasattr(self, "VD"):
return {"VD": self.VD}
if hasattr(self, "VB"):
return {"VB": self.VB}
return None

def is_engineered(self):
if self.engineered:
return True
else:
vb, vd = self.get_VB(), self.get_VD()
for var_domain in [vb, vd]:
vd, vb, = self.get_VD(), self.get_VB()
for var_domain in [vd, vb]:
if var_domain and var_domain.is_engineered():
self.engineered = True
return self.engineered
Expand All @@ -921,10 +926,10 @@ def is_engineered(self):
return False

def get_fragments(self):
vb, vd = self.get_VB(), self.get_VD()
vd, vb = self.get_VD(), self.get_VB()

# If a variable domain exists
for var_domain in [vb, vd]:
for var_domain in [vd, vb]:
if var_domain:
for frag in var_domain.get_fragments():
yield frag
Expand All @@ -951,16 +956,16 @@ def standardise_chain_names(self) -> None:
new_id = []
new_child_dict = {}

if hasattr(self, 'VB'):
new_child_dict['E'] = self.child_dict[self.VB]
self.VB = 'E'
new_id.append('E')

if hasattr(self, 'VD'):
new_child_dict['D'] = self.child_dict[self.VD]
self.VD = 'D'
new_id.append('D')

if hasattr(self, 'VB'):
new_child_dict['E'] = self.child_dict[self.VB]
self.VB = 'E'
new_id.append('E')

with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonWarning)

Expand Down
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