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: ')