def problem_prot():
''' http://rosalind.info/problems/prot/ '''
from solutions.prot import prot
f = readfile('rosalind_prot.txt')
with f:
for line in f:
lineoutput(prot(line))
def orf(dna):
''' Open reading Frames
Given: A DNA string s of length at most 1 kbp in FASTA format.
Return: Every distinct candidate protein string that can be
translated from ORFs of s. Strings can be returned in any order.
>>> dna = ('AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAG'
... 'AGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG')
>>> results = orf(dna)
>>> for r in sorted(results):
... print r
M
MGMTPRLGLESLLE
MLLGSFRLIPKETLIQVAGSSPCNLS
MTPRLGLESLLE
'''
rnadna = [rna(dna), rna(revc(dna))]
frames, results = [], []
for r in rnadna:
frames.append(r)
frames.append(r[1:])
frames.append(r[2:])
for frame in frames:
protein = prot(frame, stop=False)
for i in xrange(len(protein)):
if protein[i] == 'M':
e = protein[i:].find('$')
results.append(protein[i:i+e])
return [i for i in list(set(results)) if i != '']
def splc(dna, introns):
''' RNA Splicing
Given: A DNA string s (of length at most 1 kbp) and a
collection of substrings of s acting as introns. All
strings are given in FASTA format.
Return: A protein string resulting from transcribing and
translating the exons of s. (Note: Only one solution will
exist for the dataset provided.)
>>> dna = ('ATGGTCTACATAGCTGACAAACAGCACGTAGCAATCGGTCGAATC'
... 'TCGAGAGGCATATGGTCACATGATCGGTCGAGCGTGTTTCAAAGT'
... 'TTGCGCCTAG')
>>> introns = ['ATCGGTCGAA', 'ATCGGTCGAGCGTGT']
>>> splc(dna, introns)
'MVYIADKQHVASREAYGHMFKVCA'
'''
for intron in sorted(introns, key=len, reverse=True):
dna = ''.join(dna.split(intron))
return prot(rna(dna))