def _format_primers_report_header(self):
header_string = ''
header_string += time_hr()
header_string += wrap_text('For each degenerate primer provided, a set '
'of unambiguous primers is generated. '
'For each such set the minimum, maximum and '
'mean melting temperatures are calculated. '
'For each primer in each set stable self-'
'dimers and hairpins are predicted. '
'For every possible combination of two '
'unambiguous primers cross-dimers are also '
'predicted. If an unambiguous primer is '
'provided, it is treated as a set with a '
'single element.\n\n')
header_string += hr(' PCR conditions ')
header_string += TD_Functions.format_PCR_conditions(self._primers)+'\n'
header_string += hr(' primers and their melting temperatures ')
for primer in self._primers:
header_string += repr(primer) + '\n'
#warning
if len(self._primers) > 1:
if abs(self._primers[0].Tm_min - self._primers[1].Tm_min) >= 5:
header_string += '\nWarning: lowest melting temperatures of sense and antisense primes \n'
header_string += ' differ more then by 5C\n'
header_string += '\n'
return header_string
def _format_primers_report_header(self):
header_string = ''
header_string += time_hr()
header_string += wrap_text(
'For each degenerate primer provided, a set '
'of unambiguous primers is generated. '
'For each such set the minimum, maximum and '
'mean melting temperatures are calculated. '
'For each primer in each set stable self-'
'dimers and hairpins are predicted. '
'For every possible combination of two '
'unambiguous primers cross-dimers are also '
'predicted. If an unambiguous primer is '
'provided, it is treated as a set with a '
'single element.\n\n')
header_string += hr(' PCR conditions ')
header_string += TD_Functions.format_PCR_conditions(
self._primers) + '\n'
header_string += hr(' primers and their melting temperatures ')
for primer in self._primers:
header_string += repr(primer) + '\n'
#warning
if len(self._primers) > 1:
if abs(self._primers[0].Tm_min - self._primers[1].Tm_min) >= 5:
header_string += '\nWarning: lowest melting temperatures of sense and antisense primes \n'
header_string += ' differ more then by 5C\n'
header_string += '\n'
return header_string
def write_products_report(self):
if not self._have_results: return
#open report file
ipcr_products = self._open_report('BLAST PCR products', self._PCR_products_filename)
ipcr_products.write(time_hr())
for record_name in self._PCR_Simulations:
ipcr_products.write(hr(' query ID: %s ' % record_name, symbol='#'))
ipcr_products.write(self._PCR_Simulations[record_name].format_products_report())
ipcr_products.close()
print '\nThe list of BLAST PCR products was written to:\n ',self._PCR_products_filename
self._add_report('BLAST PCR products', self._PCR_products_filename)
def write_products_report(self):
if not self._have_results: return
#open report file
ipcr_products = self._open_report('iPCR products', self._PCR_products_filename)
ipcr_products.write(time_hr())
if self._PCR_Simulation:
ipcr_products.write(self._PCR_Simulation.format_products_report())
else: ipcr_products.write(hr(' No PCR products have been found ', symbol='!'))
ipcr_products.close()
print '\nThe list of PCR products was written to:\n %s' % self._PCR_products_filename
self._add_report('iPCR products', self._PCR_products_filename)
#end def
#end class
def write_products_report(self):
if not self._have_results: return
#open report file
ipcr_products = self._open_report('iPCR products',
self._PCR_products_filename)
ipcr_products.write(time_hr())
if self._PCR_Simulation:
ipcr_products.write(self._PCR_Simulation.format_products_report())
else:
ipcr_products.write(
hr(' No PCR products have been found ', symbol='!'))
ipcr_products.close()
print '\nThe list of PCR products was written to:\n %s' % self._PCR_products_filename
self._add_report('iPCR products', self._PCR_products_filename)
#end def
#end class
def write_report(self):
if not self._have_results: return
#open report file
report = self._open_report(self._PCR_report_suffix, self._PCR_report_filename)
if not report: return
#header
report.write(time_hr())
report.write(self._format_header())
#if no PCR products have been found
if not self._have_results:
report.write(hr(' No PCR products have been found ', symbol='!'))
report.close()
return
#report body
report.write(self._format_report_body())
report.close()
print '\n%s report was written to:\n %s' % (self._PCR_report_suffix,
self._PCR_report_filename)
report_name = self._PCR_report_suffix.replace('_', ' ').replace('-', ' ')
self._add_report(report_name, self._PCR_report_filename)
def write_report(self):
if not self._have_results: return
#open report file
report = self._open_report(self._PCR_report_suffix,
self._PCR_report_filename)
if not report: return
#header
report.write(time_hr())
report.write(self._format_header())
#if no PCR products have been found
if not self._have_results:
report.write(hr(' No PCR products have been found ', symbol='!'))
report.close()
return
#report body
report.write(self._format_report_body())
report.close()
print '\n%s report was written to:\n %s' % (
self._PCR_report_suffix, self._PCR_report_filename)
report_name = self._PCR_report_suffix.replace('_',
' ').replace('-', ' ')
self._add_report(report_name, self._PCR_report_filename)
def write_hits_report(self):
if not self._have_blast_results: return
blast_report = self._open_report('blast hits report', self._hits_report_filename)
if not blast_report: return
#header
blast_report.write(time_hr())
blast_report.write(wrap_text('All hits are filtered by dG of the annealing '
'of alignments and, if --no-exonuclease '
'option was provided, hits with mismatches on '
"3'-end are ignored.\n"))
blast_report.write('\n')
#filter parameters
blast_report.write(hr(' filtration parameters '))
if self._with_exonuclease:
blast_report.write("DNA polymerase HAS 3'-5'-exonuclease activity\n")
else: blast_report.write("DNA polymerase doesn't have 3'-5'-exonuclease activity\n")
blast_report.write('Maximum dG of an alignment: %.2f kcal/mol\n' % max_dimer_dG)
blast_report.write('\n')
blast_report.write(hr(''))
blast_report.write('\n\n')
#print records
for r, blast_record in enumerate(self._blast_results):
num_hits = len(blast_record.alignments)
blast_report.write(hr(' query ID: %s ' % blast_record.query, symbol='#'))
#filter hits by alignments and format report text for each hit
hits = []
for h in xrange(num_hits):
hit = blast_record.alignments[h]
desc = blast_record.descriptions[h]
#check and format hsps
hsps = []
for hsp in hit.hsps:
hsp_duplex = self._duplex_from_hsp(hsp)
#check if any stable dimers are formed by this duplex
if not hsp_duplex: continue
#check 3' mismatch
if not self._with_exonuclease \
and not hsp_duplex.have_3_matches: continue
#get primer concentration
for primer in self._primers:
if primer.has_subsequence(hsp_duplex.fwd_seq):
hsp_primer_concentration = primer.concentration
break
#format hsps representation
hsp_text = ('score: %d; bits: %d; E-value: %.2e;\n\n'
% (hsp.score, hsp.bits, hsp.expect))
hsp_text += hsp_duplex.print_most_stable(include_fwd_3_mismatch=self._with_exonuclease)
hsp_text += 'Conversion degree = %.2f%%\n\n' \
% (tdf.primer_DNA_conversion_degree(hsp_primer_concentration, hsp_duplex.K)*100)
hsp_text += 'Template strand: '
if hsp.frame[1] == 1:
hsp_text += 'antisense\n'
hsp_text += 'Position on template: %d ==> %d\n' \
% (hsp.sbjct_start, hsp.sbjct_end)
elif hsp.frame[1] == -1:
hsp_text += 'sense\n'
hsp_text += 'Position on template: %d <== %d\n' \
% (hsp.sbjct_start, hsp.sbjct_end)
hsp_text += hr('', '.')
hsps.append((hsp_duplex.dG, hsp_text))
#no need to include weak hits to the report
if not hsps: continue
#sort hsps by minimum dG
hsps.sort(key=lambda(x): x[0])
#format hit
hit_str = wrap_text(hit.title)+'\n'
hit_str += 'Length: %d\n' % hit.length
hit_str += 'Max bits: %d\n' % desc.bits
hit_str += 'Alignments: %d\n' % len(hit.hsps)
hit_str += '\n'
hit_str += hr(' %d alignments after filtration ' % len(hsps))
hit_str += ''.join(_hsp[1] for _hsp in hsps)[:-1]
hits.append((hsps[0][0], desc.title, desc.score, desc.bits, desc.e, len(hsps), hit_str))
if not hits:
blast_report.write(wrap_text('All hits were filtered out.\n'))
#write report to the file
else:
#print the short list of all hits
num_hits = len(hits)
num_hits_len = len(str(num_hits))
#sort hits by minimum dG
hits.sort(key=lambda(x): x[0])
#print header
blast_report.write(hr(' %d hits ' % num_hits, symbol='#'))
for h, hit in enumerate(hits):
spacer = ' '*(num_hits_len-len(str(h)))
blast_report.write(wrap_text('%d.%s %s\n'
% (h+1, spacer,
(hit[1].split('|')[-1]).strip())))
blast_report.write(('%s min dG: %.2f; score: %d; bits: %d; '
'E-value: %.2e; alignments: %d\n\n')
% (' '*num_hits_len, hit[0], hit[2],
hit[3], hit[4], hit[5]))
blast_report.write('\n')
#print each formatted hit
for h, hit in enumerate(hits):
blast_report.write(hr(' Hit #%d ' % (h+1), symbol='='))
blast_report.write(hit[6])
blast_report.write(hr('', symbol='='))
if h < num_hits-1: blast_report.write('\n\n')
blast_report.write(hr('', symbol='#'))
if r < len(self._blast_results)-1: blast_report.write('\n\n')
blast_report.close()
print '\nTop hits with top HSPs from BLAST results were written to:\n ' + \
self._hits_report_filename
self._add_report('BLAST hits', self._hits_report_filename)
