python 读入test2.fa，把每条FASTA序列连成一行然后输出

 

001、方法1

(base) root@PC1:/home/test2# ls
a.fasta  test.py
(base) root@PC1:/home/test2# cat a.fasta              ## 测试fasta文件
>gene1 myc
AGCTGCCTAAGC
GGCATAGCTAATCG
>gene2 jun
ACCGAATCGGAGCGATG
GGCATTAAAGATCTAGCT
>gene3 malat1
AGGCTAGCGAG
GCGCGAG
GATTAGGCG
(base) root@PC1:/home/test2# cat test.py                ## 测试程序
#!/usr/bin/python

in_file = open("a.fasta", "r")

idx = 0
for i in in_file:
    i = i.strip()
    if i[0] == ">":
        if idx > 0:
            print("")
        idx += 1
        print(i.split(" ")[0].split(">")[1])
    else:
        print(i, end = "")
print("")

in_file.close()
(base) root@PC1:/home/test2# python test.py           ## 执行程序
gene1
AGCTGCCTAAGCGGCATAGCTAATCG
gene2
ACCGAATCGGAGCGATGGGCATTAAAGATCTAGCT
gene3
AGGCTAGCGAGGCGCGAGGATTAGGCG

 

002、方法2

(base) root@PC1:/home/test2# ls
a.fasta  test.py
(base) root@PC1:/home/test2# cat a.fasta          ## 测试fasta文件
>gene1 myc
AGCTGCCTAAGC
GGCATAGCTAATCG
>gene2 jun
ACCGAATCGGAGCGATG
GGCATTAAAGATCTAGCT
>gene3 malat1
AGGCTAGCGAG
GCGCGAG
GATTAGGCG
(base) root@PC1:/home/test2# cat test.py           ## 测试程序
#!/usr/bin/python

in_file = open("a.fasta", "r")
dict1 = {}
for i in in_file:
    i = i.strip()
    if i[0] == ">":
        key = i.split(" ")[0].split(">")[1]
        dict1[key] = ""
    else:
        dict1[key] += i
for i,j in dict1.items():
    print(i)
    print(j)
in_file.close()
(base) root@PC1:/home/test2# python test.py       ## 执行程序
gene1
AGCTGCCTAAGCGGCATAGCTAATCG
gene2
ACCGAATCGGAGCGATGGGCATTAAAGATCTAGCT
gene3
AGGCTAGCGAGGCGCGAGGATTAGGCG

 

参考：https://www.jianshu.com/p/403a23fdd7bb