def misprime_check(self):
u = UnaFolder(
t=self.tm(),
safety=self.construct.settings.ss_safety,
mg_salt=self.construct.settings.mg_salt,
na_salt=self.construct.settings.na_salt,
)
if self.stick.top:
target = str(self.stick.cfragment.sequence())
else:
target = str(reverse_complement(Seq(self.stick.cfragment.sequence())))
if u.mis_prime(target, str(self.seq())):
self.warning.all().filter(type="mp").delete()
for warning in u.warnings:
w = Warning.objects.create(
primer=self,
type="mp",
text="Potentital mis-priming "
+ (str(warning[1]) + " bp from " if warning[1] > 0 else " of ")
+ "3' end of primer at bp "
+ str(warning[2])
+ ", length "
+ str(warning[0])
+ ", energy "
+ str(warning[3]),
)
def selfPrime(self): u = UnaFolder(t = self.fullTm(), safety=3, mg_salt=self.mg, na_salt=self.na) ret, image = u.self_prime(str(self.topPrimer())) new_image = join(settings.MEDIA_ROOT, split(image)[1]) os.rename(image, new_image) wst = '' for warning in u.warnings: wst += 'Potential self-priming of 3\' end! Length: ' + str(warning[0]) + ', dG: ' + str(warning[1]) + '<br />' return join(settings.MEDIA_URL, split(image)[1]), wst
def selfPrime(self): u = UnaFolder(t = self.fullTm(), safety=3, mg_salt=self.mg, na_salt=self.na) ret, image = u.self_prime(str(self.topPrimer())) print settings.MEDIA_ROOT os.rename(image, settings.MEDIA_ROOT+image[1::]) wst = '' for warning in u.warnings: wst += 'Potential self-priming of 3\' end! Length: ' + str(warning[0]) + ', dG: ' + str(warning[1]) + '<br />' return settings.MEDIA_URL + image, wst
def self_prime_check(self): u = UnaFolder(t=self.tm(), safety=self.construct.settings.ss_safety, mg_salt=self.construct.settings.mg_salt, na_salt=self.construct.settings.na_salt) ret, image = u.self_prime(str(self.seq())) os.rename(image, settings.MEDIA_ROOT+'unafold/p-'+str(self.id)) self.warning.all().filter(type='sp').delete() self.save() for warning in u.warnings: w = Warning.objects.create( primer = self, type = 'sp', text = 'Potential self-priming of 3\' end! Length: ' + str(warning[0]) + ', dG: ' + str(warning[1]), )
def selfPrime(self):
u = UnaFolder(t=self.fullTm(),
safety=3,
mg_salt=self.mg,
na_salt=self.na)
ret, image = u.self_prime(str(self.topPrimer()))
new_image = join(settings.MEDIA_ROOT, split(image)[1])
os.rename(image, new_image)
wst = ''
for warning in u.warnings:
wst += 'Potential self-priming of 3\' end! Length: ' + str(
warning[0]) + ', dG: ' + str(warning[1]) + '<br />'
return join(settings.MEDIA_URL, split(image)[1]), wst
def misprime_check(self): u = UnaFolder(t=self.tm(), safety=self.construct.settings.ss_safety, mg_salt=self.construct.settings.mg_salt, na_salt=self.construct.settings.na_salt) if(self.stick.top): target = str(self.stick.cfragment.sequence()) else: target = str(reverse_complement(Seq(self.stick.cfragment.sequence()))) if u.mis_prime(target, str(self.seq())): self.warning.all().filter(type='mp').delete() for warning in u.warnings: w = Warning.objects.create( primer = self, type = 'mp', text= 'Potentital mis-priming ' + (str(warning[1]) + ' bp from ' if warning[1] > 0 else ' of ') + '3\' end of primer at bp ' + str(warning[2]) + ', length ' + str(warning[0]) + ', energy ' + str(warning[3]), )
def self_prime_check(self): u = UnaFolder(t=self.tm(), safety=self.construct.settings.ss_safety, mg_salt=self.construct.settings.mg_salt, na_salt=self.construct.settings.na_salt) ret, image = u.self_prime(str(self.seq())) print os.path.join(settings.MEDIA_ROOT, 'unafold/p-%s' % self.id) os.rename(image, os.path.join(settings.MEDIA_ROOT, 'unafold/p-%s' % self.id)) self.warning.all().filter(type='sp').delete() self.save() for warning in u.warnings: w = Warning.objects.create( primer = self, type = 'sp', text = 'Potential self-priming of 3\' end! dG: %s' % warning[1], )
def self_prime_check(self): u = UnaFolder(t=self.tm(), safety=self.construct.settings.ss_safety, mg_salt=self.construct.settings.mg_salt, na_salt=self.construct.settings.na_salt) ret, image = u.self_prime(str(self.seq())) print os.path.join(settings.MEDIA_ROOT, 'unafold/p-%s' % self.id) os.rename(image, os.path.join(settings.MEDIA_ROOT, 'unafold/p-%s' % self.id)) self.warning.all().filter(type='sp').delete() self.save() for warning in u.warnings: w = Warning.objects.create( primer = self, type = 'sp', text = 'Potential self-priming of 3\' end! dG: %s' % warning[1], )
def misprime_check(self): u = UnaFolder(t=self.tm(), safety=self.construct.settings.ss_safety, mg_salt=self.construct.settings.mg_salt, na_salt=self.construct.settings.na_salt) if(self.stick.top): target = str(self.stick.cfragment.sequence()) else: target = str(reverse_complement(Seq(self.stick.cfragment.sequence()))) if u.mis_prime(target, str(self.seq())): self.warning.all().filter(type='mp').delete() for warning in u.warnings: w = Warning.objects.create( primer = self, type = 'mp', text= 'Potentital mis-priming ' + (str(warning[1]) + ' bp from ' if warning[1] > 0 else ' of ') + '3\' end of primer at bp ' + str(warning[2]) + ', length ' + str(warning[0]) + ', energy ' + str(warning[3]), )
