def makeDNASpecCompliant(sDNASeq, lFeatureMap, lDNASpec, dCFSeqs, bVerbose=True, bCheckOnly=False, dInsertIntoAndVerityOtherMaps=None):
# Redefine print function to adheal to verbose printing (voodoo magic)
print = genPrintFunc(bVerbose)
# First check DNA
print('Verifying DNA Sequence:')
tVerResult = verifyDNASpecCompliance(sDNASeq, lFeatureMap, lDNASpec, dCFSeqs, bVerbose)
# What to do
if not tVerResult[1]: # If it cannot be mutated to create valid match its invalid and return None
print('DNA sequence cannot be mutated to create valid sequence! - Returning None')
return None, None
elif tVerResult[0]: # DNA seq is valid
# # PLACEHOLDER/ NOT CURRENTLY USED Function to insert this into aditional feature specifications and verify those too
# def verifyAgainsAditionalMaps(sDNASeq, lFeatureMap, lDNASpec, dInsertIntoAndVerityOtherMaps, dCFSeqs, bVerbose=True):
# lStaticFeatureMap = list(lDNASpec)
# # First make a static DNA specification of using the iserted sequence
# for iIndex, tRegion in enumerate(lFeatureMap):
# lStaticFeatureMap[iIndex]['seq'] = sDNASeq[tRegion[0]:tRegion[1]]
sDNASeqRevComp = getReverseComplement(sDNASeq)
lRevFeatureMap = reverseFeatureMap(lFeatureMap)
print('Verifying DNA Sequence Reverse Complement:')
tRevCompVerResult = verifyDNASpecCompliance(sDNASeqRevComp, lRevFeatureMap, lDNASpec, dCFSeqs, bVerbose)
if not tRevCompVerResult[1]: # If the reverse complement cannot be mutated to create valid match its invalid and return None
print('DNA sequence reverse complement cannot be mutated to create valid sequence! - Returning None')
return None, None
elif tRevCompVerResult[0]: # DNA reverse complement is valid
print('DNA sequence and its reverse complement are bought valid! - Returning Sequence')
return sDNASeq, lFeatureMap # DNA sequence and its reverse compliment are valid thus return the sequence
# So if it doesnt return anything either the DNA sequence or its reverse complement where invalid but can be mutated to get a valid result
print('DNA sequence and/or its reverse complement are/is invalid but are bought mutable!', end='')
if bCheckOnly:
print(' - Returning None')
return None, None
print(' - Mutating Sequence')
sDNASeq, lFeatureMap = genSpecDNA(lDNASpec) # Thus generate another version of the dna
sDNASeq, lFeatureMap = makeDNASpecCompliant(sDNASeq, lFeatureMap, lDNASpec, dCFSeqs, bVerbose) # And try to make it compliant agan (gottal love recusion)
return sDNASeq, lFeatureMap
},
{ 'name' : 'Memory-ScaI',
'seq' : 'AGTACT',
'mutable' : False,
'maycontain':
[
'Memory-ScaI'
]
},
{ 'name' : 'DNARand-25',
'seq' : genRandomDNAFunction(25),
'mutable' : True,
'maycontain': []
},
{ 'name' : 'ZifBindingMotif-E2C-RC',
'seq' : getReverseComplement('GGGGCCGGAGCCGCAGTG'),
'mutable' : False,
'maycontain':
[
'Zif-E2C'
]
},
{ 'name' : 'DNARand-125',
'seq' : genRandomDNAFunction(125),
'mutable' : True,
'maycontain': []
},
{ 'name' : 'NdeI',
'seq' : 'CATATG',
'mutable' : False,
'maycontain':
},
{ 'name' : 'Memory-ScaI',
'seq' : 'AGTACT',
'mutable' : False,
'maycontain':
[
'Memory-ScaI'
]
},
{ 'name' : 'DNARand-25',
'seq' : genRandomDNAFunction(25),
'mutable' : True,
'maycontain': []
},
{ 'name' : 'ZifBindingMotif-PTF-RC',
'seq' : getReverseComplement('ATCGGCGCCGGCGACATC'),
'mutable' : False,
'maycontain':
[
'Zif-PTF'
]
},
{ 'name' : 'DNARand-125',
'seq' : genRandomDNAFunction(125),
'mutable' : True,
'maycontain': []
},
{ 'name' : 'NdeI',
'seq' : 'CATATG',
'mutable' : False,
'maycontain':
