def generate_0x1(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq):
variant = seq[:i] + seq[i + 1:]
listVariants.append(variant)
return listVariants
def generate_0x1(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq):
variant = seq[:i] + seq[i+1:]
listVariants.append(variant)
return listVariants
def generateSatLib(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listListMutations = [seqlib.allBases(rna=False)
if base == 'N' else [base]
for base in list(consensus)]
listVariants = [''.join(seq) for seq in list(product(*listListMutations))]
return listVariants
def generate_1x1(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq):
for otherBase in seqlib.allOtherBases(base, rna):
variant = seq[:i] + otherBase + seq[i + 1:]
listVariants.append(variant)
return listVariants
def generate_1x0(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq[:-1]):
for newBase in seqlib.allBases(rna):
variant = seq[:i + 1] + newBase + seq[i + 1:]
listVariants.append(variant)
return listVariants
def generateSatLib(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listListMutations = [
seqlib.allBases(rna=False) if base == 'N' else [base]
for base in list(consensus)
]
listVariants = [''.join(seq) for seq in list(product(*listListMutations))]
return listVariants
def generate_1x1(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq):
for otherBase in seqlib.allOtherBases(base, rna):
variant = seq[:i] + otherBase + seq[i+1:]
listVariants.append(variant)
return listVariants
def generate_1x0(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq[:-1]):
for newBase in seqlib.allBases(rna):
variant = seq[:i+1] + newBase + seq[i+1:]
listVariants.append(variant)
return listVariants
def generate_1x2(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq[:-1]):
nextBase = seq[i + 1]
for otherBase in seqlib.allOtherBases([base, nextBase], rna):
variant = seq[:i] + otherBase + seq[i + 2:]
listVariants.append(variant)
return listVariants
def generate_1x2(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq[:-1]):
nextBase = seq[i+1]
for otherBase in seqlib.allOtherBases([base, nextBase], rna):
variant = seq[:i] + otherBase + seq[i+2:]
listVariants.append(variant)
return listVariants
def generate_3x2(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq[:-1]):
for newBase1 in seqlib.allBases(rna):
for newBase2 in seqlib.allBases(rna):
for newBase3 in seqlib.allBases(rna):
variant = seq[:i] + newBase1 + newBase2 + newBase3 + seq[i+2:]
listVariants.append(variant)
return listVariants
def generate_2x3(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq[:-2]):
nextBase = seq[i + 1]
nextNextBase = seq[i + 2]
for otherBase1 in seqlib.allOtherBases(base, rna):
for otherBase3 in seqlib.allOtherBases(nextNextBase, rna):
variant = seq[:i] + otherBase1 + otherBase3 + seq[i + 3:]
listVariants.append(variant)
return listVariants
def generate_3x2(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq[:-1]):
for newBase1 in seqlib.allBases(rna):
for newBase2 in seqlib.allBases(rna):
for newBase3 in seqlib.allBases(rna):
variant = seq[:i] + newBase1 + newBase2 + newBase3 + seq[
i + 2:]
listVariants.append(variant)
return listVariants
def generate_2x3(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq[:-2]):
nextBase = seq[i+1]
nextNextBase = seq[i+2]
for otherBase1 in seqlib.allOtherBases(base, rna):
for otherBase3 in seqlib.allOtherBases(nextNextBase, rna):
variant = seq[:i] + otherBase1 + otherBase3 + seq[i+3:]
listVariants.append(variant)
return listVariants
def generate_4x4(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq[:-3]):
nextBase = seq[i+1]
nextNextBase = seq[i+2]
nextNextNextBase = seq[i+3]
for otherBase1 in seqlib.allOtherBases(base, rna):
for newBase2 in seqlib.allBases(rna):
for newBase3 in seqlib.allBases(rna):
for otherBase4 in seqlib.allOtherBases(nextNextNextBase, rna):
variant = seq[:i] + otherBase1 + newBase2 + newBase3 + otherBase4 + seq[i+4:]
listVariants.append(variant)
return listVariants
def generate_4x4(consensus, rna=False):
seq = seqlib.standardize(consensus, rna)
listVariants = []
for i, base in enumerate(seq[:-3]):
nextBase = seq[i + 1]
nextNextBase = seq[i + 2]
nextNextNextBase = seq[i + 3]
for otherBase1 in seqlib.allOtherBases(base, rna):
for newBase2 in seqlib.allBases(rna):
for newBase3 in seqlib.allBases(rna):
for otherBase4 in seqlib.allOtherBases(
nextNextNextBase, rna):
variant = seq[:
i] + otherBase1 + newBase2 + newBase3 + otherBase4 + seq[
i + 4:]
listVariants.append(variant)
return listVariants
