def vrc01_class_mutation_count(seqs, vgene_only=True):
input_seqs = [sequence.Sequence([s['seq_id'], s['vdj_aa']]) for s in seqs]
shared = []
total = []
# get VRC01-class sequences
vrc01_seqs = get_vrc01_class_sequences(vgene_only=vgene_only)
vrc01_names = [s.id for s in vrc01_seqs]
# get glVRC01 sequence
glvrc01 = get_vrc01_germline_sequence(vgene_only=vgene_only)
glvrc01_name = glvrc01.id
import re
regex = re.compile("[a-zA-Z]")
# identify VRC01-class mutations
for s in input_seqs:
alignment_seqs = [s] + vrc01_seqs + [glvrc01]
aln = muscle(alignment_seqs)
aln_seq = [seq for seq in aln if seq.id == s.id][0]
aln_gl = [seq for seq in aln if seq.id == glvrc01_name][0]
aln_vrc01s = [seq for seq in aln if seq.id in vrc01_names]
# Strip '-' off the front of strings based on input string
# match = re.search(regex,str(aln_seq.seq))
index = [m.start() for m in re.finditer(regex, str(aln_seq.seq))]
# Logic if no match is found...
if (len(index) > 1):
aln_seq.seq = aln_seq.seq[index[0]:(index[-1]+1)]
aln_gl.seq = aln_gl.seq[index[0]:(index[-1]+1)]
for p in aln_vrc01s:
p.seq = p.seq[index[0]:(index[-1]+1)]
# Count mutations
_total = sum([_s != g for _s, g in zip(str(aln_seq.seq), str(aln_gl.seq)) if g != '-'])
total.append(_total)
all_shared = {}
for vrc01 in aln_vrc01s:
_shared = []
for q, g, v in zip(str(aln_seq.seq), str(aln_gl.seq), str(vrc01.seq)):
if g == '-' and v == '-':
_shared.append(False)
elif q == v and q != g:
_shared.append(True)
else:
_shared.append(False)
all_shared[vrc01.id] = _shared
any_shared = 0
for pos in zip(*all_shared.values()):
if any(pos):
any_shared += 1
shared.append(any_shared)
# print("Seq: %20s, Total: %2d, Shared: %2d" % (str(aln_seq.id), _total, any_shared))
# print("Seq: "+str(aln_seq.id)+" Total: "+str(_total)+", Shared: "+str(any_shared))
return shared, total
def vrc01_class_mutation_positions(seqs, vgene_only=True):
data = []
input_seqs = [sequence.Sequence([s['seq_id'], s['vdj_aa']]) for s in seqs]
input_names = [s.id for s in input_seqs]
# get VRC01-class sequences
if (not expanded):
hiv_seqs = get_vrc01_class_sequences()
else:
hiv_seqs = get_expanded_vrc01_class_sequences()
all_hiv_names = [s.id for s in hiv_seqs]
# MSA
seqs_for_alignment = input_seqs + hiv_seqs
seqs_for_alignment.append(
get_vrc01_germline_sequence(vgene_only=vgene_only))
aln = muscle(seqs_for_alignment)
aln_seqs = [seq for seq in aln if seq.id in input_names]
aln_gl = [seq for seq in aln if seq.id == 'glVRC01'][0]
aln_mins = [seq for seq in aln if seq.id in ['minVRC01', 'min12A21']]
aln_hiv = [seq for seq in aln if seq.id in all_hiv_names]
for seq in aln_seqs:
seq_data = []
for i, (s, g) in enumerate(zip(str(seq.seq), str(aln_gl.seq))):
# if g == '-' and s == '-':
if g == '-':
continue
min_residues = [seq[i] for seq in aln_mins]
vrc01_residues = [seq[i] for seq in aln_hiv]
if s == '-':
seq_data.append(0)
elif s == g:
seq_data.append(0)
elif s != g and s in min_residues:
seq_data.append(2)
elif s != g and s in vrc01_residues:
seq_data.append(3)
elif s != g and s not in vrc01_residues:
seq_data.append(1)
else:
seq_data.append(0)
data.append(np.asarray(seq_data))
return np.asarray(data)
def identifyvrc01muts(input_seqs, vrc01_seqs, glvrc01, genecall):
import re
regex = re.compile("[a-zA-Z]")
shared = []
total = []
glvrc01_name = glvrc01.id
vrc01_names = [s.id for s in vrc01_seqs]
for s in input_seqs:
alignment_seqs = [s] + vrc01_seqs + [glvrc01]
aln = muscle(alignment_seqs)
aln_seq = [seq for seq in aln if seq.id == s.id][0]
aln_gl = [seq for seq in aln if seq.id == glvrc01_name][0]
aln_vrc01s = [seq for seq in aln if seq.id in vrc01_names]
# Strip '-' off the front of strings based on input string
# match = re.search(regex,str(aln_seq.seq))
index = [m.start() for m in re.finditer(regex, str(aln_seq.seq))]
# Logic if no match is found...
if (len(index) > 1):
aln_seq.seq = aln_seq.seq[index[0]:(index[-1] + 1)]
aln_gl.seq = aln_gl.seq[index[0]:(index[-1] + 1)]
for p in aln_vrc01s:
p.seq = p.seq[index[0]:(index[-1] + 1)]
# If there is a VH12 Mask. Generate a mask string 1 for include and 0 otherwise
chainmaskstring = "x" * len(aln_gl.seq)
usemask = False
if genecall == VH12 and vh12mask:
chainmaskstring = get_mask_string(aln_gl.seq, masks[VH12])
usemask = True
elif genecall == VK320 and vk320mask:
chainmaskstring = get_mask_string(aln_gl.seq, masks[VK320])
usemask = True
elif genecall == VK133 and vk133mask:
chainmaskstring = get_mask_string(aln_gl.seq, masks[VK133])
usemask = True
elif genecall == VL214 and vl214mask:
chainmaskstring = get_mask_string(aln_gl.seq, masks[VL214])
usemask = True
# Count mutations
_total = sum([
_s != g for _s, g in zip(str(aln_seq.seq), str(aln_gl.seq))
if g != '-'
])
total.append(_total)
all_shared = {}
for vrc01 in aln_vrc01s:
_shared = []
for q, g, v, cmask in zip(str(aln_seq.seq), str(aln_gl.seq),
str(vrc01.seq), str(chainmaskstring)):
if g == '-' and v == '-':
_shared.append(False)
elif q == v and q != g:
if not usemask:
_shared.append(True)
else:
if cmask == "1":
_shared.append(True)
else:
_shared.append(False)
else:
_shared.append(False)
all_shared[vrc01.id] = _shared
any_shared = 0
for pos in zip(*all_shared.values()):
if any(pos):
any_shared += 1
shared.append(any_shared)
# print("Seq: %20s, Total: %2d, Shared: %2d" % (str(aln_seq.id), _total, any_shared))
# print("Seq: "+str(aln_seq.id)+" Total: "+str(_total)+", Shared: "+str(any_shared))
return shared, total
