python 中统计fasta文件中每条scaffold中碱基的数目

 

001、

[root@pc1 test2]# ls
a.fa  test.py
[root@pc1 test2]# cat a.fa      ## 测试fasta文件
>chr1
aattggggc
ssff
xx
>chr2
uuuttcccccc
>chr3
ggggcccc
tttt
[root@pc1 test2]# cat test.py      ## 统计脚本
#!/usr/bin/python

in_file = open("a.fa", "r")
out_file = open("result.txt", "w")

dict1 = dict()

for i in in_file:
        i = i.strip()
        if i.startswith(">"):
                key = i
                dict1[key] = str()
        else:
                dict1[key] += i

for i,j in dict1.items():
        out_file.write(i + ":")
        print(len(j), file = out_file)

in_file.close()
out_file.close()

 

[root@pc1 test2]# ls
a.fa  test.py
[root@pc1 test2]# python test.py     ## 执行程序
[root@pc1 test2]# ls
a.fa  result.txt  test.py
[root@pc1 test2]# cat result.txt     ## 执行结果
>chr1:15
>chr2:11
>chr3:12
[root@pc1 test2]# cat a.fa        ## 原始文件
>chr1
aattggggc
ssff
xx
>chr2
uuuttcccccc
>chr3
ggggcccc
tttt

 

002、改进速度

[root@pc1 test1]# cat test.py
#!/usr/bin/python
in_file = open("a.fa", "r")
out_file = open("result.txt", "w")

dict1 = dict()

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

for i,j in dict1.items():
        out_file.write(i.split(" ")[0] + ":")
        length = 0
        for k in j:
                length += len(k)
        print(length, file = out_file)
in_file.close()
out_file.close()

 

[root@pc1 test1]# ls
a.fa  test.py
[root@pc1 test1]# ll -h        ## 测试1G参考基因组
total 1018M
-rw-r--r--. 1 root root 1018M Nov 12 20:46 a.fa
-rw-r--r--. 1 root root   391 Nov 12 20:51 test.py
[root@pc1 test1]# time python test.py   ## 测试程序

real    0m11.972s
user    0m9.793s
sys     0m2.179s
[root@pc1 test1]# ls
a.fa  result.txt  test.py