def looping_Ha_diff_species(self, nLoops):
lista = []
self.jsd = JSD.Class_JSD(self.desk)
self.entFile = bioClass.Entropy_File()
self.hmi = MI.Mutual_Information_Horizontal(self.desk,
want_nuc_aa_list=False,
want_shannon=False)
if not self.hmi.ok:
self.error_msg = 'Problems with Init_MI_Heat_Map_Hist_Graph.'
return False
specList = self.all_species.keys()
n = len(specList)
for i in range(n - 1):
for j in range(i + 1, n):
''' for each pair of species simulate Ha '''
if nLoops > 10:
nLoops = int(round(nLoops / 10.))
ret, dList = self.read_and_calc_Ha(specList[i],
specList[j],
nLoops=nLoops)
if not ret:
return None
lista.append(dList)
return lista
def __init__(self, desk):
self.desk = desk
self.dr = desk.dr
''' ------------------------------------------------------- '''
self.entFile = bioClass.Entropy_File()
self.gg = graphPac.GeneralGraphic(desk)
self.minmax = desk.minmax
def looping_JSD_one_sample(self):
self.jsd = JSD.Class_JSD(self.desk)
''' -----------------------------------------'''
self.time = crono.Timing()
self.entFile = bioClass.Entropy_File()
self.set_my_cluster_filenames()
name = '%s %s %s' % (self.desk.organism, self.gene, self.title)
self.names = [[self.cluster_input_filename, name]]
self.hmi = MI.Mutual_Information_Horizontal(self.desk,
want_nuc_aa_list=False,
want_shannon=False)
if not self.hmi.ok:
self.error_msg = 'Problems with Init_MI_Heat_Map_Hist_Graph.'
return False
if self.desk.organism == "Drosophila":
self.dr = dro.Drosophila()
# filename_dist_mat = self.cluster_input_filename
''' always read and calc in looping_JSD_one_sample'''
ret, dicMI, _, _ = self.read_and_calc_one_sample()
if not ret:
return False
xlabel = 'species x species'
ylabel = 'JSD(%s)' % (self.desk.unit)
if self.desk.showGraph or self.desk.saveGraph:
self.jsd.plot_JSD_MI(self.desk,
dicMI,
self.desk.filename_correction,
xlabel,
ylabel,
onlyRef=True,
stay=True)
return True
def looping_H0_same_species(self):
lista = []
self.jsd = JSD.Class_JSD(self)
self.filename_correction = '_bias_corr' if self.withCorrection else ''
self.entFile = bioClass.Entropy_File()
self.hmi = MI.Mutual_Information_Horizontal(self, want_nuc_aa_list=False, want_shannon = False)
if not self.hmi.ok:
self.error_msg = 'Problems with Init_MI_Heat_Map_Hist_Graph.'
return False
for spec in sorted(self.all_species.keys()):
''' for each species simulate H0 '''
# self.spRef = self.which_sp(self.organism, spec)
ret, dList = self.read_and_calc_H0(spec, 3)
if not ret:
return None
lista.append(dList)
return lista
def looping_JSD_all_samples(self):
plt.close("all")
plt.clf()
self.jsd = JSD.Class_JSD(self)
self.filename_correction = '_bias_corr' if self.withCorrection else ''
if self.withCorrection:
self.filename_correction = '_bias_corr'
else:
self.filename_correction = ''
self.time = crono.Timing()
name = '%s %s %s'%(self.organism, self.gene, self.title)
self.entFile = bioClass.Entropy_File()
self.set_my_cluster_filenames()
self.names = [[self.cluster_input_filename, name]]
self.hmi = MI.Mutual_Information_Horizontal(self, want_nuc_aa_list=False, want_shannon = False)
if not self.hmi.ok:
self.error_msg = 'Problems with Init_MI_Heat_Map_Hist_Graph.'
return False
if self.organism == "Drosophila":
self.dr = dro.Drosophila()
filename_dist_mat = self.cluster_input_filename
if not os.path.exists(self.rootTable + filename_dist_mat) or self.de_novo:
''' if not found in looping_JSD_all_samples read and calc '''
ret, dicMI, stri, sError = self.read_and_calc_all_samples()
else:
ret, dicMI, stri, sError = self.read_distance_matrix(filename_dist_mat)
if not ret:
return False
xlabel = 'species x species'
ylabel = 'JSD(%s)'%(self.unit)
if self.saveData:
self.showmsg_obs('\n ============ %s ============'%(self.striMatrix))
self.showmsg_obs(stri)
self.showmsg_obs('============ SE %s ============'%(self.striMatrix))
self.showmsg_obs(sError)
self.showmsg_obs('============ %s ============\n'%(self.striMatrix))
if not self.hmi.entFile.write_file(self.rootTable, filename_dist_mat, stri, True):
return False
filename = filename_dist_mat.replace('.txt','') + '_se.txt'
if not self.hmi.entFile.write_file(self.rootTable, filename, sError):
return False
striSummary = self.hmi.print_MI_species_data(dicMI, roundVal=self.roundVal)
filename = filename.replace('_se.txt','') + '_summary.txt'
if not self.hmi.entFile.write_file(self.rootTable, filename, striSummary, True):
return False
if self.showGraph or self.saveGraph:
self.jsd.plot_JSD_MI(self, dicMI, self.filename_correction, xlabel, ylabel, onlyRef=False )
return True
def looping(self, desk, opt):
print("-->>", opt)
plt.close("all")
plt.clf()
desk.minmax = opt[0]
if desk.each_all == 'each':
loopCorrection = [desk.withCorrection]
else:
loopCorrection = [True, False]
for correction in loopCorrection:
''' -----------------------------------------'''
desk.withCorrection = correction
self.time = timePack.Timing()
name = '%s %s %s' % (desk.organism, desk.gene, desk.title)
print 'name', name
self.entFile = bioClass.Entropy_File()
desk.set_cluster_filenames()
desk.names = [desk.cluster_input_filename, name]
self.imi = imi.Mutual_Information_Vertical(desk)
if not self.imi.ok:
self.error_msg = 'Problems with Init_MI_Heat_Map_Hist_Graph.'
return False
filename_dist_mat = desk.cluster_input_filename
if not os.path.exists(desk.rootTable +
filename_dist_mat) or desk.de_novo:
ret, dicMI, stri, sError = self.read_and_calc(desk)
else:
ret, dicMI, stri, sError = self.read_distance_matrix(
desk, filename_dist_mat)
if not ret:
return False
xlabel = 'species x species'
''' recalc: desk.title_jsd and desk.unit '''
desk.set_cluster_filenames()
ylabel = 'JSD(%s)' % (desk.unit)
desk.showmsg_obs('\n ============ %s ============' %
(desk.striMatrix))
desk.showmsg_obs(stri)
desk.showmsg_obs('============ SE %s ============' %
(desk.striMatrix))
desk.showmsg_obs(sError)
desk.showmsg_obs('============ %s ============\n' %
(desk.striMatrix))
if desk.saveData:
if not self.imi.entFile.write_file(
desk.rootTable, filename_dist_mat, stri, True):
return False
filename = filename_dist_mat.replace('.txt', '') + '_se.txt'
if not self.imi.entFile.write_file(desk.rootTable, filename,
sError):
return False
striSummary = self.imi.print_MI_species_data(
dicMI, roundVal=desk.roundVal)
filename = filename.replace('_se.txt', '') + '_summary.txt'
if not self.imi.entFile.write_file(desk.rootTable, filename,
striSummary, True):
return False
listSpecies = self.get_species(desk)
self.imi.ttest_MI_species_data(desk, listSpecies, dicMI)
if desk.showGraph or desk.saveGraph:
self.jsd.plot_JSD_MI(desk, dicMI, xlabel, ylabel)
return True
'''
Revised on 20/02/2014
@author: Flavio Lichtenstein
@local: UNIFESP - Bioinformatica
'''
import classes.BioPythonClass as bioClass
basic = bioClass.Basic()
showmessage = False
rootTable = 'C:/drosophila/files/'
randomShannonTableName = 'shannon_random_DNA_dic.txt'
entFile = bioClass.Entropy_File()
if not entFile.setNames(rootTable, randomShannonTableName):
print 'Could not open ' + rootTable + randomShannonTableName
ok, msg = entFile.read_shannon_random_file(showKeys = False)
if not ok:
print msg + ', perhaps Shannon dictionary bad formated.'
exit()
print '--------------------------------------------------------'
print 'Random h-Shannon table opened.'
print '--------------------------------------------------------'
print 'L \t entropy \t sdv \t mer%'
print '--------------------------------------------------------'