python 中统计不同scafflod的GC含量并输出GC含量最高的scafflod

 

001、方法1

root@PC1:/home/test# ls
a.fasta  test.py
root@PC1:/home/test# cat a.fasta                                   ## 测试fasta文件
>Rosalind_6404
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
TCCCACTAATAATTCTGAGG
>Rosalind_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
ATATCCATTTGTCAGCAGACACGC
>Rosalind_0808
CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
TGGGAACCTGCGGGCAGTAGGTGGAAT
root@PC1:/home/test# cat test.py                                   ## 测试程序
#!/usr/bin/python
in_file = open("a.fasta", "r")
out_file = open("result.txt", "w")
dict1 = {}
dict2 = {}

for i in in_file:
    i = i.strip()
    if i.startswith(">"):
        key = i.split(">")[1]
        dict1[key] = []
    else:
        dict1[key].append(i)
for i,j in dict1.items():
    j = "".join(j).upper()
    dict2[i] = (j.count("C") + j.count("G"))/len(j)

result = max(dict2.items(), key = lambda x: x[1])
print(result[0] + "\n" +  str(result[1]), file = out_file, end = "\n")

in_file.close()
out_file.close()
root@PC1:/home/test# python test.py                             ## 运行程序
root@PC1:/home/test# ls
a.fasta  result.txt  test.py
root@PC1:/home/test# cat result.txt                              ## 运行结果
Rosalind_0808
0.6091954022988506

 

002、方法2

root@PC1:/home/test# ls
a.fasta  test.py
root@PC1:/home/test# cat a.fasta                                   ## 测试fasta文件
>Rosalind_6404
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
TCCCACTAATAATTCTGAGG
>Rosalind_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
ATATCCATTTGTCAGCAGACACGC
>Rosalind_0808
CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
TGGGAACCTGCGGGCAGTAGGTGGAAT
root@PC1:/home/test# cat test.py                            ## 测试程序
#!/usr/bin/python

import re                                                   ## 利用re包中 findall函数查找指定的碱基数目
in_file = open("a.fasta", "r")
out_file = open("result.txt", "w")
dict1 = {}
dict2 = {}

for i in in_file:
    i = i.strip()
    if i[0] == ">":
        key = i.split(">")[1]
        dict1[key] = []
    else:
        dict1[key].append(i)

for i,j in dict1.items():
    seq = "".join(j).upper()
    gc_count = len(re.findall("[GC]", seq))
    dict2[i] = "%.4f" % (gc_count/len(seq))

result = max(dict2.items(), key = lambda x: x[1])
out_file.write(result[0] + "\n" + result[1] + "\n")

in_file.close()
out_file.close()
root@PC1:/home/test# python test.py                            ## 执行程序
root@PC1:/home/test# ls
a.fasta  result.txt  test.py
root@PC1:/home/test# cat result.txt                            ## 运行结果
Rosalind_0808
0.6092

 

003、方法3

root@PC1:/home/test# ls
a.fasta  test.py
root@PC1:/home/test# cat a.fasta                                  ## 测试fasta文件
>Rosalind_6404
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
TCCCACTAATAATTCTGAGG
>Rosalind_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
ATATCCATTTGTCAGCAGACACGC
>Rosalind_0808
CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
TGGGAACCTGCGGGCAGTAGGTGGAAT
root@PC1:/home/test# cat test.py                               ## 测试程序
#!/usr/bin/python

in_file = open("a.fasta", "r")
out_file = open("result.txt", "w")
dict1 = dict()
dict2 = dict()

for i in in_file:
    i = i.strip()
    if i.startswith(">"):
        key = i.split(">")[1]
        dict1[key] = []
    else:
        dict1[key].append(i)

for i,j in dict1.items():
    seq = "".join(j).upper()
    gc_count = 0
    for k in seq:
        if k == "G" or k == "C":
            gc_count += 1
    gc_ratio = "%.4f" % (gc_count/len(seq))
    dict2[i] = gc_ratio

result = max(dict2.items(), key = lambda x: x[1])
out_file.write(result[0] + "\n" + result[1] + "\n")

in_file.close()
out_file.close()
root@PC1:/home/test# python test.py                            ## 执行程序
root@PC1:/home/test# ls
a.fasta  result.txt  test.py
root@PC1:/home/test# cat result.txt                             ## 运行结果
Rosalind_0808
0.6092

 

参考：https://mp.weixin.qq.com/s?__biz=MzIxMjQxMDYxNA==&mid=2247484172&idx=1&sn=d8dec9ae5ffea81ef02e8f0d7ea4672b&chksm=9747ca95a030438313f483f6c62c9c32551e23682f98be6868edf423ea88180165e21c5dedc8&scene=178&cur_album_id=1635727573621997580#rd