def write_current_primers(self,filename='current_order.txt'):
"""Write currently selected primers to a space-delimited file
This is formatted to be uploaded to the MGW website for ordering"""
if not filename:
print 'no filename given'
return
if not self.primers.curselection():
print 'primer database is empty or no selection'
return
# Get currently selected primers into a list
tmp_selection=self.primers.curselection()
selection=[]
for num in tmp_selection:
selection.append(int(num))
primers={}
first=1
# Now figure out the selected primers and store them in primers
for primer_num in selection:
name_selected=self.primer_order[primer_num]
primers[name_selected]=self.parent.data['primer_dict'][name_selected]
#fd=open(filename,'wb')
self.DumpPDB = []
import mutation
for entry in primers:
tmp = []
tmp.append(entry+'_for')
tmp.append(' ')
tmp.append(primers[entry]['sequence'])
reverse=mutation.get_reverse_complementary(primers[entry]['sequence'])
tmp.append('\n')
tmp.append(entry+'_rev')
tmp.append(' ')
tmp.append(reverse)
tmp.append('\n')
self.DumpPDB.append(tmp)
try:
fd=open(filename,'a')
for line in self.DumpPDB:
str = ''
for S in line:
str = str+S
fd.write(str+'\n')
fd.close()
print "File written ",filename
except:
print "error: could not write file ",filename
from PEATDB.textFrame import textFrame
self.order_frame = textFrame(self, 'Current primers')
self.order_frame.load_text(self.DumpPDB)
fd.close()
return
def find_primer_binding_sites(self, primer_seq, DNA_seq):
'''Find all possible binding sites for the primer in the DNA_seq
- also probe the reverse strand'''
binding_sites = self.find_primer_binding_sites_1(primer_seq, DNA_seq)
# Reverse complement strand
rev_compl = mutation.get_reverse_complementary(DNA_seq)
rev_binding_sites = self.find_primer_binding_sites_1(
primer_seq, rev_compl, 1)
return binding_sites + rev_binding_sites
def find_primer_binding_sites(self,primer_seq,DNA_seq):
'''Find all possible binding sites for the primer in the DNA_seq
- also probe the reverse strand'''
binding_sites=self.find_primer_binding_sites_1(primer_seq,DNA_seq)
# Reverse complement strand
rev_compl = mutation.get_reverse_complementary(DNA_seq)
rev_binding_sites = self.find_primer_binding_sites_1(primer_seq,rev_compl,1)
return binding_sites+rev_binding_sites
def apply_primer_to_DNA(self,this_primer,DNA_seq,position):
"""Construct new DNA sequence. If we have a negative position,
then it's a reverse strand primer"""
if position<0:
import mutation
position=abs(int(position))
repl_seq=mutation.get_reverse_complementary(this_primer['sequence'])
position=len(DNA_seq)-(position+len(repl_seq))
else:
repl_seq=this_primer['sequence']
# Construct the new DNA
new_DNA=DNA_seq[:position]+repl_seq+DNA_seq[position+len(repl_seq):]
return new_DNA
def display_detailed_results(self,junk=None):
"""Figure out the selected primer and display in textbox"""
selection=int(str(self.primer_result.curselection()[0]))
name_selected=self.primer_order[selection]
this_primer=self.foundprimers[name_selected]
self.detailed_results.delete(1.0,END)
# Insert the template DNA sequence
this_primer['template_DNA']=self.data['DNAseq']
# Get the alignment
this_primer['startpos']=self.pDB.align_primer(this_primer)
# Make sure that we have the updated the characteristics of the primer
import evaluate_primer
EVAL=evaluate_primer.evaluate_primer()
hairpin,selfcompl,Tm_inpos,Tm_method_used,mismatches=EVAL.get_characteristics(this_primer,self.Tm_method.get())
this_primer['hairpin_prop']=hairpin
this_primer['self-compl']=selfcompl
# Show all the info on the primer
self.detailed_results.insert(END,'Primer: %s \n' %name_selected)
self.detailed_results.insert(END,'Length: %3d bases\n' %(len(this_primer['sequence'])))
self.detailed_results.insert(END,"Forward 5' %s 3'\n" %this_primer['sequence'])
# Show the reverse complementary sequence
import mutation
self.detailed_results.insert(END,"Reverse complementary: 5' %s 3'\n" %mutation.get_reverse_complementary(this_primer['sequence']))
# Show the characteristics of the primer
text='-----------------------\nCharacteristics\nTm (aligned): %5.2f (%s)\n' %(Tm_inpos,Tm_method_used)
self.detailed_results.insert(END,text)
text='Hairpin: %s, \nself-sim: %s, \nrestr. site differences: ' %(this_primer['hairpin_prop'],
this_primer['self-compl'])
self.detailed_results.insert(END,text)
# Show the recognition sequence for the enzyme(s)
unique_added,unique_removed,non_unique_added,non_unique_removed=self.pDB.get_primer_restriction_differences(this_primer)
enz_specs=self.RS.enzymes_regexs
inserted=None
for enz in unique_added.keys():
if enz_specs.has_key(enz):
self.detailed_results.insert(END,enz+'(+)*, ')
inserted=1
for enz in unique_removed.keys():
if enz_specs.has_key(enz):
self.detailed_results.insert(END,enz+'(-)*, ')
inserted=1
for enz in non_unique_added.keys():
if enz_specs.has_key(enz):
self.detailed_results.insert(END,enz+'(+), ')
inserted=1
for enz in non_unique_removed.keys():
if enz_specs.has_key(enz):
self.detailed_results.insert(END,enz+'(-), ')
inserted=1
# If there were no differences in the restriction map, then write that
if inserted==None:
self.detailed_results.insert(END,'None')
# Delete all graphic objects from last round
for obj in self.detailed_objs.keys():
self.seqframe.delete(obj)
# Align the primer
this_primer['startpos']=self.pDB.align_primer(this_primer)
# Draw the new primer
#print self.pDB_open.__dict__.keys()
#self.pDB.primers.selection_clear()
self.pDB_open.clear_pDB_objects()
self.pDB.display_primer(this_primer)
return
def display_detailed_results(self, junk=None):
"""Figure out the selected primer and display in textbox"""
selection = int(str(self.primer_result.curselection()[0]))
name_selected = self.primer_order[selection]
this_primer = self.foundprimers[name_selected]
self.detailed_results.delete(1.0, END)
# Insert the template DNA sequence
this_primer['template_DNA'] = self.data['DNAseq']
# Get the alignment
this_primer['startpos'] = self.pDB.align_primer(this_primer)
# Make sure that we have the updated the characteristics of the primer
import evaluate_primer
EVAL = evaluate_primer.evaluate_primer()
hairpin, selfcompl, Tm_inpos, Tm_method_used, mismatches = EVAL.get_characteristics(
this_primer, self.Tm_method.get())
this_primer['hairpin_prop'] = hairpin
this_primer['self-compl'] = selfcompl
# Show all the info on the primer
self.detailed_results.insert(END, 'Primer: %s \n' % name_selected)
self.detailed_results.insert(
END, 'Length: %3d bases\n' % (len(this_primer['sequence'])))
self.detailed_results.insert(
END, "Forward 5' %s 3'\n" % this_primer['sequence'])
# Show the reverse complementary sequence
import mutation
self.detailed_results.insert(
END, "Reverse complementary: 5' %s 3'\n" %
mutation.get_reverse_complementary(this_primer['sequence']))
# Show the characteristics of the primer
text = '-----------------------\nCharacteristics\nTm (aligned): %5.2f (%s)\n' % (
Tm_inpos, Tm_method_used)
self.detailed_results.insert(END, text)
text = 'Hairpin: %s, \nself-sim: %s, \nrestr. site differences: ' % (
this_primer['hairpin_prop'], this_primer['self-compl'])
self.detailed_results.insert(END, text)
# Show the recognition sequence for the enzyme(s)
unique_added, unique_removed, non_unique_added, non_unique_removed = self.pDB.get_primer_restriction_differences(
this_primer)
enz_specs = self.RS.enzymes_regexs
inserted = None
for enz in unique_added.keys():
if enz_specs.has_key(enz):
self.detailed_results.insert(END, enz + '(+)*, ')
inserted = 1
for enz in unique_removed.keys():
if enz_specs.has_key(enz):
self.detailed_results.insert(END, enz + '(-)*, ')
inserted = 1
for enz in non_unique_added.keys():
if enz_specs.has_key(enz):
self.detailed_results.insert(END, enz + '(+), ')
inserted = 1
for enz in non_unique_removed.keys():
if enz_specs.has_key(enz):
self.detailed_results.insert(END, enz + '(-), ')
inserted = 1
# If there were no differences in the restriction map, then write that
if inserted == None:
self.detailed_results.insert(END, 'None')
# Delete all graphic objects from last round
for obj in self.detailed_objs.keys():
self.seqframe.delete(obj)
# Align the primer
this_primer['startpos'] = self.pDB.align_primer(this_primer)
# Draw the new primer
#print self.pDB_open.__dict__.keys()
#self.pDB.primers.selection_clear()
self.pDB_open.clear_pDB_objects()
self.pDB.display_primer(this_primer)
return
def display_single_primer(self,selection,focus,delete):
"""Display a single primer - focus on it if focus is true, and delete
previous graphics and text objects if delete is true"""
name_selected=self.primer_order[selection]
#print 'SELECTION=',selection
this_primer = self.parent.data['primer_dict'][name_selected]
self.current_primers_shown.append(this_primer)
self.parent.primer_displayed=1 #tells DNAtool that a primer is currently shown
self.details.config(state=NORMAL)
if delete:
self.details.delete(1.0,END)
# Align the primer
# If we do not have a DNA sequence then we cannot do it
this_primer['startpos']=None
if self.parent.data.has_key('DNAseq'):
if self.parent.data['DNAseq']:
# Find all possible binding sites for the primer
sites=self.find_primer_binding_sites(this_primer['sequence'],self.parent.data['DNAseq'])
# Print the number of binding sites
best_score=0
best_position=None
scores=[]
first_neg=1
for position,score in sites:
scores.append(score)
# Find the best position
if score>best_score:
best_score=score
best_position=position
# Set the primer start for the primer characteristics
this_primer['startpos']=best_position
this_primer['template_DNA']=self.parent.data['DNAseq']
# Show all the info on the primer
self.details.tag_config('n', foreground='blue')
self.details.insert(END,'Primer: %s \n' %name_selected, 'n')
self.details.insert(END,'Description: %s \n' %(this_primer['description']))
self.details.insert(END,'Length: %3d bases\n' %(len(this_primer['sequence'])))
self.details.insert(END,"Forward 5' %s 3'\n\n" %this_primer['sequence'])
# Show the reverse complementary sequence
import mutation
self.details.insert(END,"Reverse complementary: 5' %s 3'\n" %mutation.get_reverse_complementary(this_primer['sequence']))
# Make sure that we have the updated the characteristics of the primer
if not this_primer.has_key('template_DNA'):
return
import evaluate_primer
EVAL=evaluate_primer.evaluate_primer()
hairpin,selfcompl,Tm_inpos,Tm_method_used,mismatches=EVAL.get_characteristics(this_primer,self.parent.Tm_method.get())
this_primer['hairpin_prop']=hairpin
this_primer['self-compl']=selfcompl
this_primer['introduced_sites']='Unknown'
# Show the characteristics of the primer
text='-----------------------\nCharacteristics\nTm (in aligned position): %5.2f (%s)\n' %(Tm_inpos,Tm_method_used)
self.details.insert(END,text)
text='Hairpin: %s, \nself-sim: %s, \nrestr. site differences: ' %(this_primer['hairpin_prop'],
this_primer['self-compl'])
self.details.insert(END,text)
# Show the recognition sequence for the enzyme(s)
self.details.insert(END,'Unique sites are marked with a "*"\n')
unique_added,unique_removed,non_unique_added,non_unique_removed=self.get_primer_restriction_differences(this_primer)
enz_specs=self.parent.RS.enzymes_regexs
inserted=None
for enz in unique_added.keys():
if enz_specs.has_key(enz):
self.details.insert(END,enz+'(+)*, ')
inserted=1
for enz in unique_removed.keys():
if enz_specs.has_key(enz):
self.details.insert(END,enz+'(-)*, ')
inserted=1
for enz in non_unique_added.keys():
if enz_specs.has_key(enz):
self.details.insert(END,enz+'(+), ')
inserted=1
for enz in non_unique_removed.keys():
if enz_specs.has_key(enz):
self.details.insert(END,enz+'(-), ')
inserted=1
# If there were no differences in the restriction map, then write that
if inserted==None:
self.details.insert(END,'None')
# Delete all graphic objects from last round
if delete:
if not getattr(self.parent,'detailed_objs',None):
self.parent.detailed_objs = {}
for obj in self.parent.detailed_objs.keys():
self.parent.seqframe.delete(obj)
if getattr(self.parent,'tempsites',None):
self.parent.tempsites.remove(obj)
# Print guidelines for this primer
scores.sort()
diff=scores[-1]-scores[-2]
self.details.insert(END,'\nDifference in # of matches between two best sites: %2d\n' %diff)
if diff<5:
self.details.insert(END,'WARNING: Primer is not unique!\n')
if scores[-1]!=len(this_primer['sequence']):
self.details.insert(END,'\nWARNING: No perfectly matching binding site.\n')
# Print the number of mismatches as a control
if this_primer['startpos']>0:
self.details.insert(END,'\nDisplaying position: %4d on forward strand\n' %this_primer['startpos'])
else:
self.details.insert(END,'\nDisplaying position: %4d on reverse strand\n' %(-this_primer['startpos']))
self.details.insert(END,'Number of mismatches: %d\n\n' %mismatches)
# Display the primer
match=self.display_primer(this_primer,focus)
# Show the binding site
self.details.insert(END,'\n==================================\n')
site=sites[0][0]
if site<0:
site=len(this_primer['sequence'])+site
#
DNA_stretch=self.parent.data['DNAseq'][site:site+len(this_primer['sequence'])]
self.details.insert(END,'Primer %s\n %s\nDNASeq %s\n' %(this_primer['sequence'],match,DNA_stretch))
# Print summary of all binding sites
self.details.insert(END,'\n---------------------\nSummary of best binding sites\n')
self.details.insert(END,'Forward strand:\n')
first_neg=1
for site,score in sites:
if site<0:
site=site*-1
if first_neg:
first_neg=None
self.details.insert(END,'Reverse compl. strand:\n')
self.details.insert(END,'Position: %4d, matches: %2d\n' %(site,score))
self.details.insert(END,'\n')
self.details.config(state=DISABLED)
# Return the sites for use in highlighting
start_position=self.get_real_primer_position(this_primer)
return [start_position,start_position+len(this_primer['sequence'])]