def remove_tumor_and_rename_decomposed(
self, tumor2seqs_with_decompose, seqs_with_ancestor, tumor_seqs,
REP, clone_frequency_for_seqs_with_ancestor):
Align = MegaAlignment()
SeqOrderIni, IniMeg2Seq = Align.name2seq(seqs_with_ancestor)
TuLs, TuMeg2Seq = Align.name2seq(tumor_seqs)
SNVNum = len(TuMeg2Seq[TuLs[0]])
IdenLs = Align.identify_similar_seq(tumor_seqs, 0)
Tu2IdenTu = Align.make_similar_seq_dic(IdenLs)
outAllSeq = ['MEGA', '!Title SNVs;', '!Format datatype=dna;', ' ']
RmCloLs = []
for Tu in tumor2seqs_with_decompose:
DeComCloLs = tumor2seqs_with_decompose[Tu]
if DeComCloLs != []:
IdenTu = Tu2IdenTu['T-' + Tu]
RmCloLs += IdenTu
RmCloLs = list(set(RmCloLs))
Done = []
for Tu in tumor2seqs_with_decompose:
DeComCloLs = tumor2seqs_with_decompose[Tu]
if RmCloLs.count(Tu) == 0:
if Done.count('#' + Tu) == 0:
outAllSeq += ['#' + Tu, TuMeg2Seq['#' + Tu]]
Done.append('#' + Tu)
if DeComCloLs != []:
DecomCloOrder, Clu2Seq = Align.name2seq(DeComCloLs)
for Clu in Clu2Seq:
Seq = Clu2Seq[Clu]
TuClu = Clu[1:].split('Clu')[0]
Code = TuClu in RmCloLs
if Code != True and Clu.find('#Node') == -1:
if Clu.find('#Clu') != -1:
Clu = '#' + Tu + Clu[1:] + 'REP' + str(REP)
if Done.count(Clu) == 0:
outAllSeq += [Clu, Seq]
Done.append(Clu)
else:
HitCloLs = clone_frequency_for_seqs_with_ancestor['T-' + Tu]
for Clo in HitCloLs:
if HitCloLs[Clo] > 0:
TuClo = Clo.split('Clu')[0]
Code = TuClo in RmCloLs
if Code != True and Clo[:4] != 'Node':
if Done.count('#' + Clo) == 0:
outAllSeq += ['#' + Clo, IniMeg2Seq['#' + Clo]]
Done.append('#' + Clo)
outAllSeq_without_redindant = Align.RmRedunSeq(outAllSeq)
outAllSeq_without_redindant += ['#hg19', ('A' * SNVNum)]
return outAllSeq_without_redindant
def AdjDecClo(self, ID, SeqLs, NodeMap, BackFor, Tree):
Align = MegaAlignment()
Ao, Anc2Seq = Align.name2seq(SeqLs)
Len = len(Anc2Seq[Ao[0]])
outNew = ['MEGA', '!Title SNVs;', '!Format datatype=dna;', ' ']
Clu2Change = {}
for Name in Anc2Seq:
if Name.find('Clu') != -1:
Clu2Change[Name] = {}
Posi = 0
while Posi < Len:
i = BackFor[Posi]
if i != ['Good']:
Change = i[0]
ChangeCloLs = i[1][0] #list
# print i,Posi
A = i[1][0][0].split('Clu')[0]
B = i[1][1][0].split('Clu')[0]
# print A,B
if (len(i[1][0]) == 1 and len(i[1][1]) == 1
and i[1][0][0].find('Clu') == -1
and i[1][1][0].find('Clu') != -1):
ChangeCloLs = i[1][1] #list
if A == B: ChangeCloLs = i[1][0]
else:
ChangeCloLs = i[1][0] #list
if A == B: ChangeCloLs = i[1][1]
#print ChangeCloLs
if Change == 'ToMut': #BC>0: #back
for Clo in ChangeCloLs:
# if Clo.find('Clu')!=-1:
if Clu2Change.has_key(Clo) != True:
Clu2Change[Clo] = {}
Clu2Change[Clo][Posi] = 'T'
if Change == 'ToWild': #MC>0: #multi
for Clo in ChangeCloLs:
# if Clo.find('Clu')!=-1:
if Clu2Change.has_key(Clo) != True:
Clu2Change[Clo] = {}
Clu2Change[Clo][Posi] = 'A'
Posi += 1
# print Clu2Change
# open('AAA','r').readlines()
for Clo in Anc2Seq:
if Clo.find('#Node') == -1:
TreeAna = TreeAnalizer()
BraLen = TreeAna.Get_branch_lenghth(Tree, Clo[1:])
# if Clo.find('Clu')!=-1 and BraLen>=1:
if BraLen >= 1 and Clu2Change.has_key(Clo):
Change = Clu2Change[Clo]
CluSeq = Anc2Seq[Clo]
Len = len(CluSeq)
c = 0
NewSeq = ''
while c < Len:
Code = c in Change
if Code == True: NewSeq += Change[c]
else: NewSeq += CluSeq[c]
c += 1
outNew += [Clo, NewSeq]
else:
outNew += [Clo, Anc2Seq[Clo]]
outNew_without_redundant_seq = Align.RmRedunSeq(outNew)
outNew_without_redundant_seq += ['#hg19', 'A' * len(Anc2Seq[Clo])]
# open('AA','r').readlines()
return outNew_without_redundant_seq