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