def main():
with open(filename) as f:
fasta = f.read()
dnas = parse_fasta_as_list(fasta)
print('\n'.join([
' '.join([str(col) for col in row]) for row in distance_matrix(dnas)
]))
def main():
with open(filename) as f:
fasta = f.read()
reads = parse_fasta_as_list(fasta)
corrections = error_corrections(reads)
for old_read, new_read in corrections.items():
print(f'{old_read}->{new_read}')
def main():
with open(filename) as f:
fasta = f.read()
dnas = parse_fasta_as_list(fasta)
a, c, g, t, consensus = consensus_and_profile(dnas)
print(''.join(consensus))
print('A:', ' '.join([str(i) for i in a]))
print('C:', ' '.join([str(i) for i in c]))
print('G:', ' '.join([str(i) for i in g]))
print('T:', ' '.join([str(i) for i in t]))
def main():
with open(filename) as f:
fasta = f.read()
dna = parse_fasta_as_list(fasta)[0]
print('\n'.join(
[' '.join(str(i) for i in site) for site in reverse_palindromes(dna)]))
def main():
with open(filename) as f:
fasta = f.read()
s1, s2 = parse_fasta_as_list(fasta)
print(transition_transversion_ratio(s1, s2))
def main(): with open(filename) as f: v, w = parse_fasta_as_list(f.read()) print(*fitting_alignment(v, w), sep='\n')
def main():
with open(filename) as f:
fasta = f.read()
s = parse_fasta_as_list(fasta)[0]
print(' '.join(map(str, failure_array(s))))
def main():
with open(filename) as f:
fasta = f.read()
dnas = parse_fasta_as_list(fasta)
print(align_strands(dnas))
def main(): with open(filename) as f: s1, s2 = parse_fasta_as_list(f.read()) print(global_alignment(s1, s2))
def main():
with open(filename) as f:
s, t = parse_fasta_as_list(f.read())
print(*global_alignment_constant_gap(s, t), sep='\n')
def main():
with open(filename) as f:
fasta = f.read()
dna = parse_fasta_as_list(fasta)[0]
print('\n'.join(open_reading_frames(dna)))
def main():
with open(filename) as f:
s1, s2 = parse_fasta_as_list(f.read())
print(*local_alignment(s1, s2), sep='\n')
def main():
with open(filename) as f:
fasta = f.read()
s, t = parse_fasta_as_list(fasta)
print(' '.join([str(i) for i in spliced_indices(s, t)]))
def main():
with open(filename) as f:
fasta = f.read()
dnas = parse_fasta_as_list(fasta)
print(longest_common_substring(dnas))
def main():
with open(filename) as f:
fasta = f.read()
dna = parse_fasta_as_list(fasta)[0]
print(' '.join([str(i) for i in kmer_composition(dna)]))
def main():
with open(filename) as f:
fasta = f.read()
dnas = parse_fasta_as_list(fasta)
print(splice(dnas)[:-1]) # exclude terminal stop
def main():
with open(filename) as f:
s1, s2 = parse_fasta_as_list(f.read())
print(edit_distance(s1, s2))
def main():
with open(filename) as f:
fasta = f.read()
rna = parse_fasta_as_list(fasta)[0]
print(perfect_matchings(rna))