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))