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_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: ')