def remove_ancestral_decomposed(self,
remove_tumor_and_rename_decomposed_seq,
Error_rate, tumor_seqs):
# print 'Tu',tumor_seqs
Align = MegaAlignment()
SeqOrderIni, Meg2Seq = Align.name2seq(
remove_tumor_and_rename_decomposed_seq)
TuLs, Tu2Seq = Align.name2seq(tumor_seqs)
good_seq = ['#MEGA', '!Title SNVs;', '!Format datatype=dna;', ' ']
RmCluClo = []
for name1 in SeqOrderIni:
if name1.find('Clu') != -1:
seq1 = Meg2Seq[name1]
for name2 in SeqOrderIni:
if name2 != '#hg19' and name1 != name2:
seq2 = Meg2Seq[name2]
Additional_mut_num1 = Align.CountAdditionalMut(
seq1, seq2)
Der = 1.0 * Additional_mut_num1 / len(seq1)
if name2.find('Clu') != -1:
if Additional_mut_num1 == 0: RmCluClo.append(name1)
else:
if Der < Error_rate: RmCluClo.append(name1)
AddedTuLs = []
for Name in SeqOrderIni:
if RmCluClo.count(Name) == 0:
good_seq += [Name, Meg2Seq[Name]]
AddedTuLs.append(Name.split('Clu')[0])
for Tu in TuLs:
if AddedTuLs.count(Tu) == 0: good_seq += [Tu, Tu2Seq[Tu]]
good_seq += ['#hg19', 'A' * len(seq1)]
return good_seq
def find_decomposed_clone(self, no_back_para_mut_decomposed_seq, REP,
Tree):
Align = MegaAlignment()
CloLs, Clo2Seq = Align.name2seq(no_back_para_mut_decomposed_seq)
DecTipLs = []
DecLs = []
DecAncLs = []
RmDecom = []
for Clo in CloLs:
# ClosestAnc = Align.find_closest_anc(Clo,Clo2Seq)
# if ClosestAnc!='' :
# DecAncLs.appned(Clo)
if Clo.find('Clu') != -1:
ID = 'REP' + str(REP)
In = -1 * len(ID)
if Clo[In:] == ID:
DecLs.append(Clo)
Posi = Tree.find(Clo[1:] + ':') + len(Clo)
# print Tree[Posi]
Go = 'y'
BraLen = ''
while Go == 'y':
BraLen += Tree[Posi]
if Tree[Posi] == ',' or Tree[Posi] == ')': Go = 'n'
Posi += 1
# print Clo,BraLen
if float(BraLen[:-1]) == 0: DecAncLs.append(Clo) ######
else: DecTipLs.append(Clo)
# print DecLs,DecAncLs
if DecLs == []: NewDecom = 'n'
elif DecTipLs != []:
NewDecom = 'y'
for Tip in DecTipLs:
TipSeq = Clo2Seq[Tip]
OriTu = Tip.split('Clu')[0]
# TipMutC
Anc = 'n'
for Clo in Clo2Seq:
if Clo != Tip: # and OriTu!=Clo:
UniNum = Align.CountAdditionalMut(TipSeq, Clo2Seq[Clo])
if UniNum == 0: Anc = 'y'
if Anc == 'y': RmDecom.append(Tip)
else: NewDecom = 'anc'
# NewDecom='anc'
# for Dclo in DecLs:
# if DecAncLs.count(Dclo)==0: NewDecom='y'
# print Clo2Seq.keys()
if RmDecom == []: NewClo2Seq_buil = no_back_para_mut_decomposed_seq
else:
NewCloDic = {}
for Clo in Clo2Seq:
if RmDecom.count(Clo) == 0: NewCloDic[Clo] = Clo2Seq[Clo]
NewClo2Seq_buil = Align.UpMeg(NewCloDic, [])
return NewDecom, RmDecom, NewClo2Seq_buil