def problem_mrna():
''' http://rosalind.info/problems/mrna/ '''
from solutions.mrna import mrna
f = readfile('rosalind_mrna.txt')
with f:
prot = f.next().strip()
lineoutput(mrna(prot) % 1000000)
def problem_rna():
''' http://rosalind.info/problems/rna/ '''
from solutions.rna import rna
f = readfile('rosalind_rna.txt')
with f:
for line in f:
lineoutput(rna(line))
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_revc():
''' http://rosalind.info/problems/revc/ '''
from solutions.revc import revc
f = readfile('rosalind_revc.txt')
with f:
for line in f:
lineoutput(revc(line))
def problem_iprb():
''' http://rosalind.info/problems/iprb/ '''
from solutions.iprb import iprb
f = readfile('rosalind_iprb.txt')
with f:
d, h, r = [int(i) for i in f.next().split()]
lineoutput(iprb(d, h, r))
def problem_hamm():
''' http://rosalind.info/problems/hamm/ '''
from solutions.hamm import hamm
f = readfile('rosalind_hamm.txt')
with f:
s, t = f.next(), f.next()
lineoutput(hamm(s, t))
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 problem_fibd():
''' http://rosalind.info/problems/fibd/ '''
from solutions.fibd import fibd
f = readfile('rosalind_fibd.txt')
with f:
m, n = [int(i) for i in f.next().split()]
lineoutput(fibd(m, n))
def problem_lia():
''' http://rosalind.info/problems/lia/ '''
from solutions.lia import lia
f = readfile('rosalind_lia.txt')
with f:
k, n = [int(i) for i in f.next().split()]
lineoutput(lia(k, n))
def problem_fib():
''' http://rosalind.info/problems/fib/ '''
from solutions.fib import fib
f = readfile('rosalind_fib.txt')
with f:
n, k = [int(i) for i in f.next().split()]
lineoutput(fib(n, k))
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_lexf():
''' http://rosalind.info/problems/lexf/ '''
from solutions.lexf import lexf
f = readfile('rosalind_lexf.txt')
with f:
lex = f.next().strip()
perm = int(f.next())
for p in lexf(lex, perm):
lineoutput(p)
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_orf():
''' http://rosalind.info/problems/orf/ '''
from solutions.orf import orf
from rutility.parsers import fasta
f = readfile('rosalind_orf.txt')
with f:
frames = orf(fasta(f).next().data)
for frame in frames:
lineoutput(frame)
def problem_lcsm():
''' http://rosalind.info/problems/lcsm/ '''
from solutions.lcsm import lcsm
from rutility.parsers import fasta
f = readfile('rosalind_lcsm.txt')
with f:
iterfasta = fasta(f)
collection = [i.data for i in iterfasta]
lineoutput(lcsm(collection))
def problem_gc():
''' http://rosalind.info/problems/gc/ '''
from solutions.gc import gc
from rutility.parsers import fasta
f = readfile('rosalind_gc.txt')
with f:
iterfasta = fasta(f)
result = max(iterfasta, key=gc)
lineoutput(result.name)
lineoutput(gc(result))
def problem_splc():
''' http://rosalind.info/problems/splc/ '''
from solutions.splc import splc
from rutility.parsers import fasta
f = readfile('rosalind_splc.txt')
with f:
iterfasta = fasta(f)
dna = iterfasta.next().data
introns = [i.data for i in list(iterfasta)]
lineoutput(splc(dna, introns))
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: ')
def problem_iev():
''' http://rosalind.info/problems/iev/ '''
from solutions.iev import iev
f = readfile('rosalind_iev.txt')
with f:
lineoutput(iev([int(i) for i in f.next().split()]))
def problem_prtm():
''' http://rosalind.info/problems/prtm/ '''
from solutions.prtm import prtm
f = readfile('rosalind_prtm.txt')
with f:
lineoutput(prtm(f.next().strip()))
