def problem_subs():
''' http://rosalind.info/problems/subs/ '''
from solutions.subs import subs
f = readfile('rosalind_subs.txt')
with f:
dna, sub = f.next(), f.next()
listoutput(subs(dna, sub))
def problem_dna():
''' http://rosalind.info/problems/dna/ '''
from solutions.dna import dna
f = readfile('rosalind_dna.txt')
with f:
for line in f:
listoutput(dna(line))
def problem_revp():
''' http://rosalind.info/problems/revp/ '''
from solutions.revp import revp
from rutility.parsers import fasta
f = readfile('rosalind_revp.txt')
with f:
iterfasta = fasta(f)
for result in revp(iterfasta.next().data):
listoutput(result)
def problem_grph():
''' http://rosalind.info/problems/grph/ '''
from solutions.grph import grph
from rutility.parsers import fasta
f = readfile('rosalind_grph.txt')
with f:
iterfasta = fasta(f)
gs = grph(iterfasta, 3)
for g in gs:
listoutput(g)
def problem_perm():
''' http://rosalind.info/problems/perm/ '''
from solutions.perm import perm
f = readfile('rosalind_perm.txt')
with f:
n = int(f.next())
total, perms = perm(n)
lineoutput(total)
for p in perms:
listoutput(p)
def problem_mprt():
''' http://rosalind.info/problems/mprt/ '''
from solutions.mprt import mprt
from rutility.parsers import uniprot
f = readfile('rosalind_mprt.txt')
with f:
for line in f:
prot = uniprot(line.strip())
locations = mprt(prot.data, 'N{P}[ST]{P}')
if locations:
lineoutput(line.strip())
listoutput(locations)
def problem_cons():
''' http://rosalind.info/problems/cons/ '''
from solutions.cons import cons
from rutility.parsers import fasta
f = readfile('rosalind_cons.txt')
with f:
iterfasta = fasta(f)
collection = [i.data for i in iterfasta]
consensus, matrix = cons(collection)
lineoutput(consensus)
listoutput(matrix[0], prefix='A: ')
listoutput(matrix[1], prefix='C: ')
listoutput(matrix[2], prefix='G: ')
listoutput(matrix[3], prefix='T: ')
