import REVC;
import codons;
import string;
import re;
if __name__ == '__main__':
pattern = r'(?=(M[^\.]*\.))'
with open("rosalind_orf.txt") as spec:
dna = spec.readline().strip()
#dna = 'AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG'
print dna
rna = string.replace(dna, 'T', 'U')
result = {}
trans = codons.proteinFromCodons(codons.splitCodons(rna))
for p in [match.group(1)[:-1] for match in re.finditer(pattern, trans)]:
result[p] = 1
trans = codons.proteinFromCodons(codons.splitCodons(rna, 1))
for p in [match.group(1)[:-1] for match in re.finditer(pattern, trans)]:
result[p] = 1
trans = codons.proteinFromCodons(codons.splitCodons(rna, 2))
for p in [match.group(1)[:-1] for match in re.finditer(pattern, trans)]:
result[p] = 1
rna = string.replace(REVC.revc(dna), 'T', 'U')
trans = codons.proteinFromCodons(codons.splitCodons(rna))
for p in [match.group(1)[:-1] for match in re.finditer(pattern, trans)]:
result[p] = 1
'''
from itertools import chain
from codons import splitCodons
from codons import proteinFromCodons
with open("rosalind_splc.txt") as spec:
seq = spec.readline().strip()
exons = [exon.strip() for exon in spec]
print "Seq (len {0}):".format(len(seq)), seq
print exons
introns = [seq]
print introns
for ex in exons:
sp = [intr.split(ex) for intr in introns]
introns = list(chain.from_iterable((sp)))
print introns
dna = "".join(introns)
print "DNA: ", dna
# Convert DNA to RNA
rna = dna.replace('T', 'U')
print "RNA: ", rna
codons = splitCodons(rna)
protein = proteinFromCodons(codons)
print
print protein[:-1]
'''
from itertools import chain
from codons import splitCodons
from codons import proteinFromCodons
with open("rosalind_splc.txt") as spec:
seq = spec.readline().strip()
exons = [exon.strip() for exon in spec]
print "Seq (len {0}):".format(len(seq)), seq
print exons
introns = [ seq ]
print introns
for ex in exons:
sp = [intr.split(ex) for intr in introns]
introns = list(chain.from_iterable((sp)))
print introns
dna = "".join(introns)
print "DNA: ", dna
# Convert DNA to RNA
rna = dna.replace('T', 'U')
print "RNA: ", rna
codons = splitCodons(rna)
protein = proteinFromCodons(codons)
print
print protein[:-1]
import REVC
import codons
import string
import re
if __name__ == '__main__':
pattern = r'(?=(M[^\.]*\.))'
with open("rosalind_orf.txt") as spec:
dna = spec.readline().strip()
#dna = 'AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG'
print dna
rna = string.replace(dna, 'T', 'U')
result = {}
trans = codons.proteinFromCodons(codons.splitCodons(rna))
for p in [
match.group(1)[:-1] for match in re.finditer(pattern, trans)
]:
result[p] = 1
trans = codons.proteinFromCodons(codons.splitCodons(rna, 1))
for p in [
match.group(1)[:-1] for match in re.finditer(pattern, trans)
]:
result[p] = 1
trans = codons.proteinFromCodons(codons.splitCodons(rna, 2))
for p in [
match.group(1)[:-1] for match in re.finditer(pattern, trans)
]: