thanks kim.. On Sat, Feb 6, 2010 at 2:36 AM, Namshin Kim <deepr...@gmail.com> wrote:
> I think you need to give arguments. > > [deepr...@s50 ~]$ python tt.py 2 4 20 > 0 1 > TCCAAGG > sequence identity to next sequence : 0.285714285714 > 2 As 2 Cs 2 Gs 1 Ts > None > ACCCGTTCTACTAGT > 3 As 5 Cs 2 Gs 5 Ts > None > > > > > On Sat, Feb 6, 2010 at 6:22 PM, chintan pathak < > chintanpatha...@gmail.com> wrote: > >> Hi guys, >> >> When I run the below code it gives me an index error: *List Index out of >> range* at setsize = int(sys.argv[1]) in the code >> >> Can you help me fix the problem. >> >> >> import random >> import sys >> >> #function that simulates the DNA sequence >> def simulate_sequence(length): >> dna = ['A', 'C', 'G', 'T'] >> sequence = '' >> for i in range(length): >> sequence += random.choice(dna) >> return sequence >> >> #function that determines the nucleotide frequencies >> def nucleotide_percentage(sequence): >> print str(sequence.count('A')) + ' As ', >> print str(sequence.count('C')) + ' Cs ', >> print str(sequence.count('G')) + ' Gs ', >> print str(sequence.count('T')) + ' Ts' >> >> #function that determines the sequence identities >> def sequence_identity(set): >> iden = [] >> count = 0.0 >> for x in range(len(set)-1): >> print str(x), str(x+1) >> for n in range(len(set[x])): >> if set[x][n] == set[x+1][n]: >> count += 1 >> iden.append(count/len(set[x])) >> count = 0.0 >> return iden >> >> >> #get three values from the parameters >> >> *setsize = int(sys.argv[1])* #number of sequences to simulate >> minlength = int(sys.argv[2]) #minimum sequence length >> maxlength = int(sys.argv[3]) #maximum sequence length >> >> sequenceset = [] >> for i in range(setsize): >> rlength = random.randint(minlength, maxlength) >> sequenceset.append(simulate_sequence(rlength)) >> >> identity = sequence_identity(sequenceset) >> >> #print the results >> for i in range(len(sequenceset)): >> print sequenceset[i] >> if i < len(sequenceset)-1: >> print 'sequence identity to next sequence : ' + str(identity[i]) >> print nucleotide_percentage(sequenceset[i]) >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "pygr-dev" group. >> To post to this group, send email to pygr-...@googlegroups.com. >> To unsubscribe from this group, send email to >> pygr-dev+unsubscr...@googlegroups.com<pygr-dev%2bunsubscr...@googlegroups.com> >> . >> For more options, visit this group at >> http://groups.google.com/group/pygr-dev?hl=en. >> > > -- > You received this message because you are subscribed to the Google Groups > "pygr-dev" group. > To post to this group, send email to pygr-...@googlegroups.com. > To unsubscribe from this group, send email to > pygr-dev+unsubscr...@googlegroups.com<pygr-dev%2bunsubscr...@googlegroups.com> > . > For more options, visit this group at > http://groups.google.com/group/pygr-dev?hl=en. > -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-...@googlegroups.com. To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en.