def foun(file: str):
"""The Founder Effect and Genetic Drift"""
l1, l2 = Parser(file).lines()
n, m = [int(x) for x in l1.split()]
a = [int(x) for x in l2.split()]
for x in pr.foun(n, m, a):
print(*[round(f, 8) for f in x])
def rstr(file: str):
"""Matching Random Motifs"""
l1, seq = Parser(file).lines()
n, x = map(float, l1.split(" "))
gc = sum([seq.count(x) for x in "GC"])
lam = ((1 - x) / 2) ** (len(seq) - gc) * (x / 2) ** gc * n
print(1 - math.exp(-lam))
def conv(file: str):
"""Comparing Spectra with the Spectral Convolution"""
l1, l2 = Parser(file).lines()
s1 = list(map(float, l1.split()))
s2 = list(map(float, l2.split()))
res = mass.conv(s1, s2)
print(res[1], res[0], sep="\n")
def lexf(file: str):
"""Enumerating k-mers Lexicographically"""
l1, l2 = Parser(file).lines()
set = l1.split(" ")
n = int(l2)
perm = ["".join(x) for x in product(set, repeat=n)]
print(*sorted(perm), sep="\n")
def lgis(file: str):
"""Longest Increasing Subsequence"""
data = Parser(file).lines()[1]
data = [int(x) for x in data.split(" ")]
s1 = ros.lgis(data)
print(*s1)
s2 = ros.lgis([-x for x in data])
s2 = [-x for x in s2]
print(*s2)
def cons(file: str):
"""Consensus and Profile"""
x = Parser(file).seqs()
mat = ros.profile_matrix(x)
print(ros.consensus_sequence(mat))
for i in range(0, 4):
print("ACGT"[i] + ":", *mat[i])
def perm(file: str):
"""Enumerating Gene Orders"""
n = Parser(file).ints()[0]
perm = list(permutations(range(1, n + 1)))
print(len(perm))
for i in perm:
print(*i)
def sign(file: str):
"""Enumerating Oriented Gene Orderings"""
n = Parser(file).ints()[0]
res = com.sign(n)
print(len(res))
for i in res:
print(*i)
def gaff(file: str):
"""Global Alignment with Scoring Matrix and Affine Gap Penalty"""
seqs = Parser(file).seqs()
res = aln.gaff(seqs[0], seqs[1], -11, -1)
print(res["dist"])
print(res["a1"])
print(res["a2"])
def seto(file: str):
"""Introduction to Set Operations"""
n, s1, s2 = Parser(file).lines()
n = int(n)
s1 = builtins.eval(s1)
s2 = builtins.eval(s2)
s3 = set(range(1, n + 1))
print(*[s1 | s2, s1 & s2, s1 - s2, s2 - s1, s3 - s1, s3 - s2], sep="\n")
def mprt(file: str):
"""Finding a Protein Motif"""
for id in Parser(file).lines():
seq = ros.get_uniprot(id)
matches = ros.find_protein_motif(str(seq.seq))
if len(matches):
print(id)
print(*matches)
def splc(file: str):
"""RNA Splicing"""
def trim(gene, intron):
s = gene.find(intron)
return gene[:s] + gene[s + len(intron) :]
seqs = Parser(file).seqs()
print(ros.Dna(reduce(trim, seqs)).translate())
def sseq(file: str):
"""Finding a Spliced Motif"""
def matches(s1, s2):
i, j = 0, 0
while j < len(s2):
if s2[j] == s1[i]:
yield i + 1
j += 1
i += 1
s1, s2 = [x.seq for x in Parser(file).fastas()]
print(*list(matches(s1, s2)))
def kmer(file: str):
"""k-Mer Composition"""
seq = Parser(file).fastas()[0].seq
# initialise hash with all possible 4-mers permutations
d = {k: 0 for k in ros.kmer_perm(4)}
# Run through 4-mer slices of sequence and increment dictionary keys
for i in range(len(seq) - 3):
d[seq[i : (i + 4)]] += 1
print(*d.values())
def iprb(file: str):
"""Mendel's First Law"""
print(pr.iprb(*Parser(file).ints()))
def lexv(file: str):
"""Ordering Strings of Varying Length Lexicographically"""
l1, l2 = Parser(file).lines()
print(*ros.lexv(l1.split(), int(l2)), sep="\n")
def pmch(file: str):
"""Perfect Matchings and RNA Secondary Structures"""
print(com.pmch(Parser(file).seqs()[0]))
def motz(file: str):
"""Motzkin Numbers and RNA Secondary Structures"""
print(com.motz(Parser(file).seqs()[0]))
def lcsq(file: str):
"""Locating Motifs Despite Introns"""
print(aln.lcsq(*Parser(file).seqs()))
def wfmd(file: str):
"""The Wright-Fisher Model of Genetic Drift"""
print(pr.wfmd(*Parser(file).ints()))
def sexl(file: str):
"""Sex-Linked Inheritance"""
arr = Parser(file).floats()
print(*[round(2 * v * (1 - v), 3) for v in arr])
def grph(file: str):
"""Overlap Graphs"""
fa = Parser(file).fastas()
for i in graph.overlap_graph(fa):
print(*i)
def prot(file: str):
"""Translating RNA into Protein"""
print(Parser(file).rna().translate())
def gcon(file: str):
"""Global Alignment with Constant Gap Penalty"""
seqs = Parser(file).seqs()
print(aln.gcon(seqs[0], seqs[1]))
def subs(file: str):
"""Finding a Motif in DNA"""
s1, s2 = Parser(file).lines()
print(*list(ros.find_motif(s1, s2)))
def eval(file: str):
"""Expected Number of Restriction Sites"""
n, s, a = Parser(file).lines()
n = int(n)
a = map(float, a.split())
print(*[round(pr.eval(n, s, x), 3) for x in a])
def fibd(file: str):
"""Mortal Fibonacci Rabbits"""
print(com.fibd(*Parser(file).ints()))
def indc(file: str):
"""Independent Segregation of Chromosomes"""
print(*pr.indc(*Parser(file).ints()))
def iev(file: str):
"""Calculating Expected Offspring"""
print(pr.iev(Parser(file).ints()))
def hamm(file: str):
"""Counting Point Mutations"""
print(aln.hamm(*Parser(file).lines()))