def find_N_glycosylation_motif(protein):
finds = []
for pos in substring_find(protein, 'N'):
if len(protein[pos-1:pos + 3]) == 4:
if (protein[pos] != 'P' and protein[pos + 1] in ('S', 'T')
and protein[pos + 2] != 'P'):
finds.append(pos)
return finds
def adjacency_list(seqs):
vertex = set()
for seq in seqs:
seq_data = seqs[seq]
overlap_seq = int(ceil(len(seq_data) / 2))
adjs = set(seqs.keys())
adjs.remove(seq)
for adj in adjs:
overlap = overlap_seq
adj_data = seqs[adj]
overlap_adj = int(ceil(len(adj_data) / 2))
if overlap < overlap_adj:
overlap = overlap_adj
pos = list(substring_find(seq_data, adj_data[:overlap]))
if pos:
vertex.add((seq, adj, pos[-1]))
return vertex
def kmer_composition(dna_string):
output = []
for p in lexf_order(4, 'ACGT'):
pos = list(substring_find(dna_string, ''.join(p)))
output.append(str(len(pos)))
return output
from prot import prepare_codon_table
from revp import read_fasta
from revc import reverse_complement
from rna import rna_transcription
from subs import substring_find
if __name__ == "__main__":
with open(os.path.join('data', 'rosalind_orf.txt')) as dataset:
seqs = read_fasta(dataset)
codon_table = prepare_codon_table(os.path.join('data', 'codon_table'))
output = []
dna = seqs.popitem()[1]
rna = (rna_transcription(dna), rna_transcription(reverse_complement(dna)))
for seq in rna:
for offset in (0, 1, 2):
for start_pos in substring_find(seq[offset:], 'AUG'):
current = []
for codon in (seq[i:i + 3]
for i in range(start_pos, len(seq), 3)):
if len(codon) == 3:
if codon_table[codon] == 'Stop' and current:
output.append(''.join(current))
current = []
elif codon == 'AUG' or current:
current.append(codon_table[codon])
print("\n".join(set(output)))
from prot import prepare_codon_table
from revp import read_fasta
from revc import reverse_complement
from rna import rna_transcription
from subs import substring_find
if __name__ == "__main__":
with open(os.path.join("data", "rosalind_orf.txt")) as dataset:
seqs = read_fasta(dataset)
codon_table = prepare_codon_table(os.path.join("data", "codon_table"))
output = []
dna = seqs.popitem()[1]
rna = (rna_transcription(dna), rna_transcription(reverse_complement(dna)))
for seq in rna:
for offset in (0, 1, 2):
for start_pos in substring_find(seq[offset:], "AUG"):
current = []
for codon in (seq[i : i + 3] for i in range(start_pos, len(seq), 3)):
if len(codon) == 3:
if codon_table[codon] == "Stop" and current:
output.append("".join(current))
current = []
elif codon == "AUG" or current:
current.append(codon_table[codon])
print("\n".join(set(output)))
