Problem
The GC-content of a DNA string is given by the percentage of symbols in the string that are ‘C‘ or ‘G‘. For example, the GC-content of "AGCTATAG" is 37.5%. Note that the reverse complement of any DNA string has the same GC-content.
DNA strings must be labeled when they are consolidated into a database. A commonly used method of string labeling is called FASTA format. In this format, the string is introduced by a line that begins with ‘>‘, followed by some labeling information. Subsequent lines contain the string itself; the first line to begin with ‘>‘ indicates the label of the next string.
In Rosalind‘s implementation, a string in FASTA format will be labeled by the ID "Rosalind_xxxx", where "xxxx" denotes a four-digit code between 0000 and 9999.
Given: At most 10 DNA strings in FASTA format (of length at most 1 kbp each).
Return: The ID of the string having the highest GC-content, followed by the GC-content of that string. Rosalind allows for a default error of 0.001 in all decimal answers unless otherwise stated; please see the note on absolute error below.
Sample Dataset
>Rosalind_6404 CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC TCCCACTAATAATTCTGAGG >Rosalind_5959 CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT ATATCCATTTGTCAGCAGACACGC >Rosalind_0808 CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC TGGGAACCTGCGGGCAGTAGGTGGAAT
Sample Output
Rosalind_0808 60.919540 方法一：
# -*- coding: utf-8 -*-
# to open FASTA format sequence file:
s=open(‘Computing_GC_Content.txt‘,‘r‘).readlines()
# to create two lists, one for names, one for sequences
name_list=[]
seq_list=[]
data=‘‘ # to put the sequence from several lines together
for line in s:
line=line.strip()
for i in line:
if i == ‘>‘:
name_list.append(line[1:])
if data:
seq_list.append(data) #将每一行的的核苷酸字符串连接起来
data=‘‘ # 合完后data 清零
break
else:
line=line.upper()
if all([k==k.upper() for k in line]): #验证是不是所有的都是大写
data=data+line
seq_list.append(data) # is there a way to include the last sequence in the for loop?
GC_list=[]
for seq in seq_list:
i=0
for k in seq:
if k=="G" or k==‘C‘:
i+=1
GC_cont=float(i)/len(seq)*100.0
GC_list.append(GC_cont)
m=max(GC_list)
print name_list[GC_list.index(m)] # to find the index of max GC
print "{:0.6f}".format(m) # 保留6位小数