def save(self, *args, **kwargs):
if not self.pk: # so it's an INSERT, not UPDATE
self.sequenceIdNo = self.sequenceListing.sequenceTotalQuantity + 1
self.sequenceListing.sequenceTotalQuantity += 1
self.sequenceListing.save()
self.residues = util.expandFormula(self.residues)
self.length = len(self.residues)
super(Sequence, self).save(*args, **kwargs)
def clean(self):
if self.moltype == 'AA':
p = pattern_prt
else:
p = pattern_nuc
self.residues = util.expandFormula(self.residues)
if not p.match(self.residues):
raise ValidationError('Enter a valid residue symbol.')
def test_expandFormula(self):
"""
Test that a formula of type MARRST(ATWQ)2..9TFSRA is correctly expanded.
"""
print 'Running %s ...' % getName()
self.assertEqual('abc', util.expandFormula('abc'))
self.assertEqual('abcddd', util.expandFormula('abc(d)3'))
self.assertEqual('abcdededede', util.expandFormula('abc(de)4'))
self.assertEqual('abcdedededefg', util.expandFormula('abc(de)4fg'))
self.assertEqual('abcdededededede', util.expandFormula('abc(de)2..6'))
self.assertEqual('abcdedededededefg', util.expandFormula('abc(de)2..6fg'))
self.assertEqual('ab(c', util.expandFormula('ab(c'))
self.assertEqual('a(b9c', util.expandFormula('a(b9c'))
def test_expandFormula(self):
"""
Test that a formula of type MARRST(ATWQ)2..9TFSRA is correctly expanded.
"""
print 'Running %s ...' % getName()
self.assertEqual('abc', util.expandFormula('abc'))
self.assertEqual('abcddd', util.expandFormula('abc(d)3'))
self.assertEqual('abcdededede', util.expandFormula('abc(de)4'))
self.assertEqual('abcdedededefg', util.expandFormula('abc(de)4fg'))
self.assertEqual('abcdededededede', util.expandFormula('abc(de)2..6'))
self.assertEqual('abcdedededededefg',
util.expandFormula('abc(de)2..6fg'))
self.assertEqual('ab(c', util.expandFormula('ab(c'))
self.assertEqual('a(b9c', util.expandFormula('a(b9c'))
def save(self, *args, **kwargs):
if not self.pk: # so it's an INSERT, not UPDATE
self.sequenceIdNo = self.sequenceListing.sequenceTotalQuantity + 1
self.sequenceListing.sequenceTotalQuantity += 1
self.sequenceListing.save()
self.residues = util.expandFormula(self.residues)
self.length = len(self.residues)
shortNuc = self.moltype in [util.MOLTYPE_DNA, util.MOLTYPE_RNA
] and self.length < 10
shortPrt = self.moltype in [util.MOLTYPE_AA] and self.length < 4
if shortNuc or shortPrt:
self.skipped = True
# I think elif is not needed TODO: perhaps there is a better way to write this condition ...
# elif self.skipped != True:
# self.skipped = False
super(Sequence, self).save(*args, **kwargs)
def clean(self):
if self.moltype == 'AA':
p = pattern_prt
else:
p = pattern_nuc
self.residues = util.expandFormula(self.residues)
