def get_vrc01class_germline_lights(clone=VK320):
vk3_20_gl = ('IGKV3-20',
'EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSP')
vk1_33_gl = ('IGKV1-33',
'DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLP')
vl2_14_gl = ('IGLV2-14',
'QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYEVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTL')
vk1_5_gl = ('IGKV1-5', 'DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNSYS')
all = [('IGKV3-20',
'EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSP'),
('IGKV1-33',
'DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLP'),
('IGLV2-14',
'QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYEVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTL')
]
if clone == VK320:
lights = sequence.Sequence(vk3_20_gl)
elif clone == VK133:
lights = sequence.Sequence(vk1_33_gl)
elif clone == VL214:
lights = sequence.Sequence(vl2_14_gl)
elif clone == VK15:
lights = sequence.Sequence(vk1_5_gl)
else:
lights = [sequence.Sequence(s) for s in all]
return lights
def get_vrc01_class_sequences(chain='heavy', vgene_only=True, only_include=None):
if vgene_only:
heavy = [('VRC01',
'QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTR'),
('PGV04',
'QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCAR'),
('VRC-CH31',
'QVQLVQSGAAVRKPGASVTVSCKFAEDDDYSPYWVNPAPEHFIHFLRQAPGQQLEWLAWMNPTNGAVNYAWYLNGRVTATRDRSMTTAFLEVKSLRSDDTAVYYCAR'),
('3BNC60',
'QVHLSQSGAAVTKPGASVRVSCEASGYKISDHFIHWWRQAPGQGLQWVGWINPKTGQPNNPRQFQGRVSLTRQASWDFDTYSFYMDLKAVRSDDTAIYFCAR'),
('12A12',
'HLVQSGTQVKKPGASVRISCQASGYSFTDYVLHWWRQAPGQGLEWMGWIKPVYGARNYARRFQGRINFDRDIYREIAFMDLSGLRSDDTALYFCAR'),
('PGV20',
'QVHLMQSGTEMKKPGASVRVTCQTSGYTFSDYFIHWLRQVPGRGFEWMGWMNPQWGQVNYARTFQGRVTMTRDVYREVAYLDLRSLTFADTAVYFCAR')]
light = []
else:
heavy = [('VRC01',
'QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVSS'),
('PGV04',
'QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSS'),
('VRC-CH31',
'QVQLVQSGAAVRKPGASVTVSCKFAEDDDYSPYWVNPAPEHFIHFLRQAPGQQLEWLAWMNPTNGAVNYAWYLNGRVTATRDRSMTTAFLEVKSLRSDDTAVYYCARAQKRGRSEWAYAHWGQGTPVVVSS'),
('3BNC60',
'QVHLSQSGAAVTKPGASVRVSCEASGYKISDHFIHWWRQAPGQGLQWVGWINPKTGQPNNPRQFQGRVSLTRQASWDFDTYSFYMDLKAVRSDDTAIYFCARQRSDFWDFDVWGSGTQVTVSS'),
('12A12',
'HLVQSGTQVKKPGASVRISCQASGYSFTDYVLHWWRQAPGQGLEWMGWIKPVYGARNYARRFQGRINFDRDIYREIAFMDLSGLRSDDTALYFCARDGSGDDTSWHLDPWGQGTLVIVSA'),
('PGV20',
'QVHLMQSGTEMKKPGASVRVTCQTSGYTFSDYFIHWLRQVPGRGFEWMGWMNPQWGQVNYARTFQGRVTMTRDVYREVAYLDLRSLTFADTAVYFCARRMRSQDREWDFQHWGQGTRIIVSS')]
light = []
seqs = heavy if chain == 'heavy' else light
if only_include is not None:
if type(only_include) in [str, unicode]:
only_include = [only_include, ]
seqs = [s for s in seqs if s[0] in only_include]
return [sequence.Sequence(s) for s in seqs]
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 get_vrc01_germline_sequence(vgene_only=True):
if vgene_only:
# gl_vrc01 = ('glVRC01', 'QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCAR')
# Hack to get to work with JH sequences. Issue is that alignment is stuid sometimes at the N-term
gl_vrc01 = ('glVRC01', 'PGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCAR')
else:
gl_vrc01 = ('glVRC01', 'QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGKNSDYNWDFQHWGQGTLVTVSS')
return sequence.Sequence(gl_vrc01)
def vrc01_class_mutation_count(seqs, vgene_only=True):
input_seqs = [sequence.Sequence([s['seq_id'], s['vdj_aa']]) for s in seqs]
# get VRC01-class sequences
if (not expanded):
vrc01_seqs = get_vrc01_class_sequences(vgene_only=vgene_only)
else:
vrc01_seqs = get_expanded_vrc01_class_sequences(vgene_only=vgene_only)
# get glVRC01 sequence
glvrc01 = get_vrc01_germline_sequence(vgene_only=vgene_only)
return identifyvrc01muts(input_seqs, vrc01_seqs, glvrc01, VH12)
def get_expanded_vrc01_class_sequences(chain='heavy', vgene_only=True, only_include=None):
heavy = [('VRC01', 'QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTR'),
('PGV04', 'QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCAR'),
('VRC-CH31', 'QVQLVQSGAAVRKPGASVTVSCKFAEDDDYSPYWVNPAPEHFIHFLRQAPGQQLEWLAWMNPTNGAVNYAWYLNGRVTATRDRSMTTAFLEVKSLRSDDTAVYYCAR'),
('3BNC60', 'QVHLSQSGAAVTKPGASVRVSCEASGYKISDHFIHWWRQAPGQGLQWVGWINPKTGQPNNPRQFQGRVSLTRQASWDFDTYSFYMDLKAVRSDDTAIYFCAR'),
('12A12', 'HLVQSGTQVKKPGASVRISCQASGYSFTDYVLHWWRQAPGQGLEWMGWIKPVYGARNYARRFQGRINFDRDIYREIAFMDLSGLRSDDTALYFCAR'),
('PGV20', 'QVHLMQSGTEMKKPGASVRVTCQTSGYTFSDYFIHWLRQVPGRGFEWMGWMNPQWGQVNYARTFQGRVTMTRDVYREVAYLDLRSLTFADTAVYFCAR'),
('PCIN63-71Ja','QVQLVQSGAEVKKPGASVRVSCKASGYTFNSCLIHWWRQAPGQGLQWMAWINPLHGAVNYAHQFQGRITVTRDTSIDTAYMELRGLRSDDTATYYCTR')]
light = []
seqs = heavy if chain == 'heavy' else light
if only_include is not None:
if type(only_include) in [str, unicode]:
only_include = [only_include, ]
seqs = [s for s in seqs if s[0] in only_include]
return [sequence.Sequence(s) for s in seqs]
def vrc01_class_mutation_count_light_chain(seqs, vgene_only=True, vgene=VK320):
input_seqs = [sequence.Sequence([s['seq_id'], s['vdj_aa']]) for s in seqs]
shared = []
total = []
# get VRC01-class sequences
if(not expanded):
vrc01_seqs = get_vrc01_class_sequences(chain=vgene, vgene_only=vgene_only)
else:
vrc01_seqs = get_expanded_vrc01_class_sequences(vgene_only=vgene_only)
# get glVRC01 sequence
glvrc01 = get_vrc01class_germline_lights(vgene)
return identifyvrc01muts(input_seqs, vrc01_seqs, glvrc01, vgene)
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 _schief_output_line(seq,
legacy,
pairisvrc01class=False,
s=None,
t=None,
m=None):
if seq is None:
return [''] * 34
line = []
line.append(seq.fraction)
line.append(seq.confidence)
line.append(seq['v_gene']['gene'])
line.append(_get_alternates(seq['v_gene']['others'], j_gene=False))
if seq['chain'] == 'heavy':
line.append(seq['d_gene']['gene'] if 'd_gene' in seq else '')
line.append(
_get_alternates(seq['d_gene']['others'], j_gene=False
) if 'd_gene' in seq else '')
line.append(seq['j_gene']['gene'])
line.append(_get_alternates(seq['j_gene']['others'], j_gene=True))
line.append(seq['cdr3_len'] if 'cdr3_len' in seq else '')
line.append(seq['cdr3_nt'].upper() if 'cdr3_nt' in seq else '')
line.append(seq['cdr3_aa'].upper() if 'cdr3_aa' in seq else '')
line.append(seq['junc_aa'])
line.append(seq['junc_nt'])
line.append('|'.join(
str(i['was']) + str(i['position']) + str(i['is'])
for i in seq['var_muts_nt']['muts']) if 'var_muts_nt' in seq else '')
line.append('|'.join(
str(i['was']) + str(i['position']) + str(i['is'])
for i in seq['var_muts_aa']['muts']) if 'var_muts_aa' in seq else '')
if seq['chain'] == 'heavy':
line.append('Data Not Available')
line.append('Data Not Available')
# D Mutations are currently not avaialbe in Abstar
# line.append('|'.join(str(i['was']) + str(i['position']) + str(i['is']) for i in seq['d_muts_nt']['muts']) if 'd_muts_nt' in seq else '')
# line.append('|'.join(str(i['was']) + str(i['position']) + str(i['is']) for i in seq['d_muts_aa']['muts']) if 'd_muts_aa' in seq else '')
line.append('|'.join(
str(i['was']) + str(i['position']) + str(i['is'])
for i in seq['join_muts_nt']['muts']) if 'join_muts_nt' in seq else '')
line.append('|'.join(
str(i['was']) + str(i['position']) + str(i['is'])
for i in seq['join_muts_aa']['muts']) if 'join_muts_aa' in seq else '')
line.append(100. - seq['nt_identity']['v'])
line.append(_get_fr_identity(seq, res='nt'))
line.append(100. - seq['aa_identity']['v'])
line.append(_get_fr_identity(seq, res='aa'))
if seq['chain'] == 'heavy':
if pairisvrc01class:
justvgene = seq['v_gene']['aa_sequence']
name = seq['seq_id']
trimmed = sequence.Sequence(justvgene)
trimmed['seq_id'] = name
trimmed['vdj_aa'] = justvgene
vrc01_class, total = vrc01_class_mutation_count([trimmed],
vgene_only=True)
muts = vrc01_class_mutation_positions([trimmed], vgene_only=True)
s.extend(vrc01_class)
t.extend(total)
m.extend(muts)
line.append(vrc01_class[0])
else:
line.append('')
line.append('yes' if 'v_ins' in seq else '')
line.append('yes' if 'v_del' in seq else '')
line.append(seq['vdj_aa'])
line.append(seq['vdj_nt'])
if 'v_ins' in seq:
len_field = 'len' if legacy else 'length'
line.append(len(seq['v_ins']))
line.append('[' + ' '.join([
str(i[len_field]) + ":" + str(i['position']) for i in seq['v_ins']
]) + ']')
else:
line.append('0')
line.append('')
if 'v_del' in seq:
len_field = 'len' if legacy else 'length'
line.append(len(seq['v_del']))
line.append('[' + ' '.join([
str(i[len_field]) + ":" + str(i['position']) for i in seq['v_del']
]) + ']')
else:
line.append('0')
line.append('')
line.append(seq['vdj_aa'].upper().count('C') if 'vdj_aa' in seq else '')
line.append(seq['cdr3_aa'].upper().count('C') if 'cdr3_aa' in seq else '')
return line
num_of_tokens = len(tokens)
if num_of_tokens != 3:
return dict(cluster_fraction=tokens[0])
else:
return dict(cluster_fraction=tokens[1], cluster_confidence=tokens[2])
seqs = []
basename = os.path.splitext(os.path.basename(sys.argv[1]))[0]
with open(sys.argv[1]) as f:
for line in f:
if line.strip() == "":
continue
d = json.loads(line.strip())
# Bryan has a pair object
seq = sequence.Sequence(d)
seqs.append(seq)
force_all_heavy_as_vrc01class = False
if (len(sys.argv) > 2):
if sys.argv[2] == "forcevrc01":
force_all_heavy_as_vrc01class = True
colortouse = '#45bc70'
if (len(sys.argv) > 3):
if sys.argv[3] == "orange":
colortouse = '#f99248'
else:
colortouse = str(sys.argv[3]).strip()
# munge the ids and create a dictionary from which we construct
def get_vrc01_class_sequences(chain='heavy',
vgene_only=True,
only_include=None):
if vgene_only:
heavy = [
('VRC01',
'QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTR'
),
('PGV04',
'QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCAR'
),
('VRC-CH31',
'QVQLVQSGAAVRKPGASVTVSCKFAEDDDYSPYWVNPAPEHFIHFLRQAPGQQLEWLAWMNPTNGAVNYAWYLNGRVTATRDRSMTTAFLEVKSLRSDDTAVYYCAR'
),
('3BNC60',
'QVHLSQSGAAVTKPGASVRVSCEASGYKISDHFIHWWRQAPGQGLQWVGWINPKTGQPNNPRQFQGRVSLTRQASWDFDTYSFYMDLKAVRSDDTAIYFCAR'
),
('12A12',
'HLVQSGTQVKKPGASVRISCQASGYSFTDYVLHWWRQAPGQGLEWMGWIKPVYGARNYARRFQGRINFDRDIYREIAFMDLSGLRSDDTALYFCAR'
),
('PGV20',
'QVHLMQSGTEMKKPGASVRVTCQTSGYTFSDYFIHWLRQVPGRGFEWMGWMNPQWGQVNYARTFQGRVTMTRDVYREVAYLDLRSLTFADTAVYFCAR'
)
]
vk3_20_light = [
('VRC01',
'EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKR'
),
('PGV04',
'EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRR'
),
('3BNC60',
'DIQMTQSPSSLSARVGDTVTITCQANGYLNWYQQRRGKAPKLLIYDGSKLERGVPARFSGRRWGQEYNLTINNLQPEDVATYFCQVYEFIVPGTRLDLKRTVAA'
)
]
vk1_33_light = [
('VRC-CH31',
'DIQMTQSPSSLSASLGDRVTITCQASRGIGKDLNWYQQKAGKAPKLLVSDASTLEGGVPSRFSGSGFHQNFSLTISSLQAEDVATYFCQQYETFGQGTKVDIK'
),
('12A12',
'DIQMTQSPSSLSASVGDRVTITCQAGQGIGSSLQWYQQKPGKAPKLLVHGASNLHRGVPSRFSGSGFHTTFSLTISGLQRDDFATYFCAVLEFFGPGTKVEIKRTVAAPSV'
)
]
vl2_14_light = [(
'PGV20',
'QSALTQPPSVSGSPGQSITLSCTGASTSVAWYQQYADKAPRLIVFDGNKRPSDISSRFSGSQSGGTASLTISGLQSEDEAYYHCNAFEFFGGGTKLTVL'
)]
light = []
else:
heavy = [
('VRC01',
'QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVSS'
),
('PGV04',
'QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSS'
),
('VRC-CH31',
'QVQLVQSGAAVRKPGASVTVSCKFAEDDDYSPYWVNPAPEHFIHFLRQAPGQQLEWLAWMNPTNGAVNYAWYLNGRVTATRDRSMTTAFLEVKSLRSDDTAVYYCARAQKRGRSEWAYAHWGQGTPVVVSS'
),
('3BNC60',
'QVHLSQSGAAVTKPGASVRVSCEASGYKISDHFIHWWRQAPGQGLQWVGWINPKTGQPNNPRQFQGRVSLTRQASWDFDTYSFYMDLKAVRSDDTAIYFCARQRSDFWDFDVWGSGTQVTVSS'
),
('12A12',
'HLVQSGTQVKKPGASVRISCQASGYSFTDYVLHWWRQAPGQGLEWMGWIKPVYGARNYARRFQGRINFDRDIYREIAFMDLSGLRSDDTALYFCARDGSGDDTSWHLDPWGQGTLVIVSA'
),
('PGV20',
'QVHLMQSGTEMKKPGASVRVTCQTSGYTFSDYFIHWLRQVPGRGFEWMGWMNPQWGQVNYARTFQGRVTMTRDVYREVAYLDLRSLTFADTAVYFCARRMRSQDREWDFQHWGQGTRIIVSS'
)
]
light = []
if chain == 'heavy':
seqs = heavy
elif chain == VK320:
seqs = vk3_20_light
elif chain == VK133:
seqs = vk1_33_light
elif chain == VL214:
seqs = vl2_14_light
else:
seqs = light
if only_include is not None:
if type(only_include) in [str, unicode]:
only_include = [
only_include,
]
seqs = [s for s in seqs if s[0] in only_include]
return [sequence.Sequence(s) for s in seqs]
