def compare_good_posi_number(self, Initial, After, IniSeq_buil,
AftSeq_buil):
IniCou = self.count_good_posi(Initial)
AftCou = self.count_good_posi(After)
Align = MegaAlignment()
CloLs, IniSeq_dic = Align.name2seq(IniSeq_buil)
CloLs, AftSeq_dic = Align.name2seq(AftSeq_buil)
ShareIni = Align.GetSharePosi1(IniSeq_dic, 'A')
ShareAft = Align.GetSharePosi1(AftSeq_dic, 'A')
print IniCou, AftCou, len(ShareIni), len(ShareAft)
if IniCou > AftCou or len(ShareAft) > len(ShareIni): AfterGood = 'n'
else: AfterGood = 'y'
return AfterGood
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