def templet_generation_and_prediction(finger_sequence, finger_name,len_minimum, len_maximum, operation_tm, C_Na,C_Mg,C_Strand):
if template_trigger_gengerate(finger_sequence,finger_name,len_maximum,len_minimum)==1: #gengerate trigger, template successfully and stored in ~tri.txt, ~tem.txt
dic_therm=unafold_pred('~tem.txt',"~tri.txt",operation_tm, C_Na,C_Mg,C_Strand)
dic_jf={}
dic_tri={}
dic_temp={}
dic_trigen={}
for cur_record_o in SeqIO.parse(open('~tem.txt'), "fasta") :
dic_temp[str(cur_record_o.id)]=str(cur_record_o.seq)
for cur_record_o in SeqIO.parse(open('~tri.txt'), "fasta") :
dic_tri[str(cur_record_o.id)]=str(cur_record_o.seq)
for cur_record_o in SeqIO.parse(open('~tri_gen.txt'), "fasta") :
dic_trigen[str(cur_record_o.id)]=str(cur_record_o.seq)
for cur_record_o in SeqIO.parse(open('~tem.txt'), "fasta") :
cur_seq=str(cur_record_o.seq).upper() #all capitalized
dic_jf[cur_record_o.id]=SeqDep.method_2_prediction(cur_seq)
for key,value in sorted(dic_therm. iteritems(), key=lambda(k,v):(v,k)):
valuelist=key.split('_')
part='_'.join(valuelist[0:5])
part2=part+'_'
triname=part2+'tri_'
triname=triname+valuelist[6]
trigenname=part2+'tri_gen'
if (float(dic_therm[key][0])>configure_finger.min_tri_temp_tm and float(dic_therm[key][0])<configure_finger.max_tri_temp_tm and float(dic_therm[key][1])<configure_finger.max_temp_tm and int(dic_therm[key][2])<configure_finger.max_temp_bonds):
#if(float(dic_therm[key][0])>configure_finger.min_tri_temp_tm and float(dic_therm[key][0])<configure_finger.max_tri_temp_tm and float(dic_therm[key][1])<configure_finger.max_temp_tm):
todo.Tritemp(finger_id=valuelist[1],type=valuelist[2], start= valuelist[3], trigger =dic_tri[triname] , trig_gen=dic_trigen[trigenname],temp=dic_temp[key],tri_length=len(dic_tri[triname]) ,temp_bayes_class=dic_jf[key][1][0],temp_pwm_class=dic_jf[key][0][0] ,temp_p90_score=dic_jf[key][0][1],temp_diff_score= dic_jf[key][0][2],tri_temp_tm=dic_therm[key][0] ,temp_tm=dic_therm[key][1] ,bonds=dic_therm[key][2] )
elixir.session.commit
def savefilebrower_all(self):
print "entered savefilebrower_all"
fName = QtGui.QFileDialog.getSaveFileName(self, "Save as xls file", "Save as new file", self.tr("Text Files (*.xls)"))
#print "step5", globals()
if fName.isEmpty() == False:
Expar.write_xls(str(fName),self, todo.Task.query.all(), todo.Tritemp.query.all())
#t=file1+'simple.xls'
#rb = xlrd.open_workbook(t)
#wb = copy(rb)
#print(rb.sheet_by_index(0).cell(0,0).value)
#wb.save(fName)
print(fName)
print('is generated!')
QtGui.QMessageBox.about(self, "Saved", "%s is generated!" % (fName))
#SeqDep.delete_file('~') # delete all the files under this folder and begins with '~'
SeqDep.delete_file2()
self.close()
exit()
def submit2(self):
self.ui.progressBar.hide()
iterator = QtGui.QTreeWidgetItemIterator(self.dialog.ui.list)
task_list={}
while True:
value = iterator.value()
if value is None:
break
if value.checkState(0):
task_list[str(value.text(0))]=1
else:
print ""
iterator.__iadd__(1)
if task_list==[]:
return
#print task_list
self.dialog2 = QtGui.QDialog()
self.dialog2.ui = Ui_Dialog2()
self.dialog2.ui.setupUi(self.dialog2)
QtCore.QObject.connect(self.dialog2.ui.pushButton, QtCore.SIGNAL("clicked()"), self.savefilebrower_all)
for finger in todo.Task.query.all():
if task_list.has_key(str(finger.finger_id)):
if str(finger.finger_type)=='HTH':
QtGui.QMessageBox.warning(Form,"Warning", "HTH fingerprinting sites may take a long time to process!")
break
for finger in todo.Task.query.all():
self.tick.emit(1)
SeqDep.delete_file('~tem')
SeqDep.delete_file('~tri')
if task_list.has_key(str(finger.finger_id)):
name='seq_'+str(finger.finger_id)+'_'+str(finger.finger_type)+'_'+str(finger.start)+'_'+str(finger.length)
finger.done=True
elixir.session.commit
Expar_database.templet_generation_and_prediction(finger.sequence, name, int(self.ui.lineEdit_9.text()),int(self.ui.lineEdit_10.text()), float(self.ui.lineEdit_11.text()), float(self.ui.lineEdit_12.text()),float(self.ui.lineEdit_13.text()),float(self.ui.lineEdit_7.text()))
#Expar_database.templet_generation_and_prediction(finger.sequence, name,8, 30, 37, 0,1,0.00000005)
for tritemp in todo.Tritemp.query.all():
item=QtGui.QTreeWidgetItem([str(tritemp.finger_id),str(tritemp.type),str(tritemp.start),str(tritemp.trig_gen),str(tritemp.trigger),str(tritemp.temp), str(tritemp.temp_bayes_class),str(tritemp.temp_pwm_class), str(tritemp.temp_p90_score),str(tritemp.temp_diff_score),str(tritemp.tri_temp_tm),str(tritemp.temp_tm),str(tritemp.bonds)])
self.dialog2.ui.list.sortByColumn(0, QtCore.Qt.AscendingOrder)
self.dialog2.ui.list.addTopLevelItem(item)
self.dialog2.ui.list.setSortingEnabled(True)
self.dialog2.ui.list.setColumnWidth(4,250)
#print SeqDep.method_2_prediction(finger.sequence)
print "************************************\nDone!\n**************************************\n"
self.dialog2.exec_()
def savefilebrower_all(self):
print "entered savefilebrower_all"
fName = QtGui.QFileDialog.getSaveFileName(
self, "Save as xls file", "Save as new file",
self.tr("Text Files (*.xls)"))
#print "step5", globals()
if fName.isEmpty() == False:
Expar.write_xls(str(fName), self, todo.Task.query.all(),
todo.Tritemp.query.all())
#t=file1+'simple.xls'
#rb = xlrd.open_workbook(t)
#wb = copy(rb)
#print(rb.sheet_by_index(0).cell(0,0).value)
#wb.save(fName)
print(fName)
print('is generated!')
QtGui.QMessageBox.about(self, "Saved",
"%s is generated!" % (fName))
#SeqDep.delete_file('~') # delete all the files under this folder and begins with '~'
SeqDep.delete_file2()
self.close()
exit()
def submit2(self):
self.ui.progressBar.hide()
iterator = QtGui.QTreeWidgetItemIterator(self.dialog.ui.list)
task_list = {}
while True:
value = iterator.value()
if value is None:
break
if value.checkState(0):
task_list[str(value.text(0))] = 1
else:
print ""
iterator.__iadd__(1)
if task_list == []:
return
#print task_list
self.dialog2 = QtGui.QDialog()
self.dialog2.ui = Ui_Dialog2()
self.dialog2.ui.setupUi(self.dialog2)
QtCore.QObject.connect(self.dialog2.ui.pushButton,
QtCore.SIGNAL("clicked()"),
self.savefilebrower_all)
for finger in todo.Task.query.all():
if task_list.has_key(str(finger.finger_id)):
if str(finger.finger_type) == 'HTH':
QtGui.QMessageBox.warning(
Form, "Warning",
"HTH fingerprinting sites may take a long time to process!"
)
break
for finger in todo.Task.query.all():
self.tick.emit(1)
SeqDep.delete_file('~tem')
SeqDep.delete_file('~tri')
if task_list.has_key(str(finger.finger_id)):
name = 'seq_' + str(finger.finger_id) + '_' + str(
finger.finger_type) + '_' + str(finger.start) + '_' + str(
finger.length)
finger.done = True
elixir.session.commit
Expar_database.templet_generation_and_prediction(
finger.sequence, name, int(self.ui.lineEdit_9.text()),
int(self.ui.lineEdit_10.text()),
float(self.ui.lineEdit_11.text()),
float(self.ui.lineEdit_12.text()),
float(self.ui.lineEdit_13.text()),
float(self.ui.lineEdit_7.text()))
#Expar_database.templet_generation_and_prediction(finger.sequence, name,8, 30, 37, 0,1,0.00000005)
for tritemp in todo.Tritemp.query.all():
item = QtGui.QTreeWidgetItem([
str(tritemp.finger_id),
str(tritemp.type),
str(tritemp.start),
str(tritemp.trig_gen),
str(tritemp.trigger),
str(tritemp.temp),
str(tritemp.temp_bayes_class),
str(tritemp.temp_pwm_class),
str(tritemp.temp_p90_score),
str(tritemp.temp_diff_score),
str(tritemp.tri_temp_tm),
str(tritemp.temp_tm),
str(tritemp.bonds)
])
self.dialog2.ui.list.sortByColumn(0, QtCore.Qt.AscendingOrder)
self.dialog2.ui.list.addTopLevelItem(item)
self.dialog2.ui.list.setSortingEnabled(True)
self.dialog2.ui.list.setColumnWidth(4, 250)
#print SeqDep.method_2_prediction(finger.sequence)
print "************************************\nDone!\n**************************************\n"
self.dialog2.exec_()
def templet_generation_and_prediction(finger_sequence, finger_name,len_minimum, len_maximum, operation_tm, C_Na,C_Mg,C_Strand):
rank=finger_name.split("_")[1]
type=finger_name.split("_")[2]
location=finger_name.split("_")[3]
length=len(finger_sequence)
trigger=[]
template=[]
maximum=int(len_maximum)
minimum=int(len_minimum)
nc=['A','T','G','C']
xxxx=['']
if (type=='HTH'):
tri_gen=finger_sequence[length-9-8:length-9]
tri_gen_len=len(tri_gen)
for i in range(minimum,maximum+1):
if (length-9-i>=9):
up_trigger=finger_sequence[length-9-i:length-9]
bottom_trigger=revcomp(finger_sequence[9:i+9])
for j in range(4):
for h in range(4):
for k in range(4):
for m in range(4):
xxxx=nc[j]+nc[h]+nc[k]+nc[m]
up_emplate=up_trigger+'GAGTC'+xxxx+up_trigger
bottom_template=bottom_trigger+'GAGTC'+xxxx+bottom_trigger
#print "<tr><td>",up_trigger,"</td><td>",revcomp(up_template),"<td><tr>"
up_set=cal_tm_bond(up_trigger,revcomp(up_template),1000,0,50)
up_pred=SeqDep.method_2_prediction(str(up_template).upper())
bottom_set=cal_tm_bond(up_trigger,revcomp(up_template),C_Na*1000,C_Mg*1000,C_Strand*1000000000)
bottom_pred=SeqDep.method_2_prediction(str(up_template).upper())
print up_trigger, revcomp(up_template), up_set[0], configure_finger.min_tri_temp_tm, float(up_set[0]), configure_finger.max_tri_temp_tm, float(up_set[1]), configure_finger.max_temp_tm , int(up_set[2]), configure_finger.max_temp_bonds
if (float(up_set[0])>configure_finger.min_tri_temp_tm and float(up_set[0])<configure_finger.max_tri_temp_tm and float(up_set[1])<configure_finger.max_temp_tm and int(up_set[2])<configure_finger.max_temp_bonds):
todo.Tritemp(finger_id=rank,type=type, start= location, trigger =up_trigger , trig_gen=tri_gen,temp=up_template,tri_length=tri_gen_len ,temp_bayes_class=up_pred[1],temp_pwm_class=up_pred[0][0] ,temp_p90_score=up_pred[0][1],temp_diff_score= up_pred[0][2],tri_temp_tm=up_set[0] ,temp_tm=up_set[1] ,bonds=up_set[2] )
elixir.session.commit
if (float(bottom_set[0])>configure_finger.min_tri_temp_tm and float(bottom_set[0])<configure_finger.max_tri_temp_tm and float(bottom_set[1])<configure_finger.max_temp_tm and int(bottom_set[2])<configure_finger.max_temp_bonds):
todo.Tritemp(finger_id=rank,type=type, start= location, trigger =bottom_trigger , trig_gen=tri_gen,temp=bottom_template, tri_length=tri_gen_len ,temp_bayes_class=bottom_pred[1],temp_pwm_class=bottom_pred[0][0] ,temp_p90_score=bottom_pred[0][1],temp_diff_score= bottom_pred[0][2],tri_temp_tm=bottom_set[0] ,temp_tm=bottom_set[1] ,bonds=bottom_set[2] )
elixir.session.commit
if (type=='HTT'):
tri_gen=finger_sequence[length-9-8:length-4]
len_tri_gen=len(tri_gen)
#print "HTT enter"
for i in range(minimum,maximum+1):
if (length-9-i>=9):
up_trigger=finger_sequence[length-9-i:length-9]
xxxx=finger_sequence[length-4:length]
up_template=up_trigger+'GAGTC'+xxxx+up_trigger
up_set=cal_tm_bond(up_trigger,revcomp(up_template),C_Na*1000,C_Mg*1000,C_Strand*1000000000)
up_pred=SeqDep.method_2_prediction(str(up_template).upper())
if (float(up_set[0])>configure_finger.min_tri_temp_tm and float(up_set[0])<configure_finger.max_tri_temp_tm and float(up_set[1])<configure_finger.max_temp_tm and int(up_set[2])<configure_finger.max_temp_bonds):
todo.Tritemp(finger_id=rank,type=type, start= location, trigger =up_trigger , trig_gen=tri_gen,temp=bottom_template,tri_length=tri_gen_len ,temp_bayes_class=up_pred[0],temp_pwm_class=up_pred[1] ,temp_p90_score=up_pred[0][1],temp_diff_score= up_pred[0][2],tri_temp_tm=up_set[0] ,temp_tm=up_set[1] ,bonds=up_set[2] )
elixir.session.commit
if (type=='TTH'):
for i in range(minimum,maximum+1):
if (length-9-i>=9):
bottom_trigger=revcomp(finger_sequence[9:i+9])
xxxx=revcomp(finger_sequence[0:4])
bottom_template=bottom_trigger+'GAGTC'+xxxx+bottom_trigger
bottom_set=cal_tm_bond(bottom_trigger,revcomp(bottom_template),C_Na*1000,C_Mg*1000,C_Strand*1000000000)
bottom_pred=SeqDep.method_2_prediction(str(bottom_template).upper())
if (float(bottom_set[0])>configure_finger.min_tri_temp_tm and float(bottom_set[0])<configure_finger.max_tri_temp_tm and float(bottom_set[1])<configure_finger.max_temp_tm and int(bottom_set[2])<configure_finger.max_temp_bonds):
todo.Tritemp(finger_id=rank,type=type, start= location, trigger =bottom_trigger , trig_gen=tri_gen,temp=bottom_template, tri_length=tri_gen_len ,temp_bayes_class=bottom_pred[1],temp_pwm_class=bottom_pred[0][0] ,temp_p90_score=bottom_pred[0][1],temp_diff_score= bottom_pred[0][2],tri_temp_tm=bottom_set[0] ,temp_tm=bottom_set[1] ,bonds=bottom_set[2] )
elixir.session.commit
