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 __init__(self, cluster_information, original_seq, tumor_seq, tsp_list,
clone_frequency_cutoff, CNV_info, ReadCountTable):
self.Tu2Cluster = cluster_information
self.CNV_info = CNV_info
self.ReadCountTable = ReadCountTable
Align = MegaAlignment()
self.OriAncOrder, self.OriAnc2Seq0 = Align.name2seq(original_seq)
self.TOrder, self.T2Seq = Align.name2seq(tumor_seq)
self.SharePosi = Align.GetSharePosi1(self.OriAnc2Seq0, 'T')
self.all_tsp = tsp_information(tsp_list)
self.CloFreCutOff = clone_frequency_cutoff
self.v_obs = self.all_tsp.tumor2alt_frequency()
identical_seq_list = Align.identify_similar_seq(tumor_seq, 0)
self.identical_seq = Align.make_similar_seq_dic(identical_seq_list)
self.freq_cutoff = self.CloFreCutOff