python 中输出fasta文件的反向序列

 

001、

root@PC1:/home/test# ls
a.fasta  test.py
root@PC1:/home/test# cat test.py               ## 测试程序
#1/usr/bin/python

in_file = open("a.fasta", "r")
dict1 = dict()

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

for i,j in dict1.items():
    print(i)
    for k in j:
        print(k)

in_file.close()
root@PC1:/home/test# cat a.fasta               ## 测试fasta文件
>gene1 myc
AGCTGCCTAAGC
GGCATAGCTAATCG
>gene2 jun
ACCGAATCGGAGCGATG
GGCATTAAAGATCTAGCT
>gene3 malat1
AGGCTAGCGAG
GCGCGAG
GATTAGGCG
root@PC1:/home/test# python test.py             ## 执行程序
>gene1 myc
CGAATCCGTCGA
GCTAATCGATACGG
>gene2 jun
GTAGCGAGGCTAAGCCA
TCGATCTAGAAATTACGG
>gene3 malat1
GAGCGATCGGA
GAGCGCG
GCGGATTAG

 

002、同时去互补序列

root@PC1:/home/test# ls
a.fasta  test.py
root@PC1:/home/test# cat test.py                              ## 测试程序
#1/usr/bin/python

in_file = open("a.fasta", "r")
dict1 = dict()

for i in in_file:
    i = i.strip()
    if i[0] == ">":
        key = i
        dict1[key] = []
    else:
        temp = i[::-1].replace("A","t").replace("T","a").replace("G","c").replace("C","g").upper()
        dict1[key].append(temp)

for i,j in dict1.items():
    print(i)
    for k in j:
        print(k)

in_file.close()
root@PC1:/home/test# cat a.fasta                                ## 测试fasta文件
>gene1 myc
AGCTGCCTAAGC
GGCATAGCTAATCG
>gene2 jun
ACCGAATCGGAGCGATG
GGCATTAAAGATCTAGCT
>gene3 malat1
AGGCTAGCGAG
GCGCGAG
GATTAGGCG
root@PC1:/home/test# python test.py                             ## 执行程序
>gene1 myc
GCTTAGGCAGCT
CGATTAGCTATGCC
>gene2 jun
CATCGCTCCGATTCGGT
AGCTAGATCTTTAATGCC
>gene3 malat1
CTCGCTAGCCT
CTCGCGC
CGCCTAATC

 

003、同时指定每行输出的碱基数目

root@PC1:/home/test# ls
a.fasta  test.py
root@PC1:/home/test# cat test.py                               ## 测试程序
#1/usr/bin/python

in_file = open("a.fasta", "r")
dict1 = dict()

for i in in_file:
    i = i.strip()
    if i[0] == ">":
        key = i
        dict1[key] = []
    else:
        temp = i[::-1].replace("A","t").replace("T","a").replace("G","c").replace("C","g").upper()
        dict1[key].append(temp)

for i,j in dict1.items():
    print(i)
    j = "".join(j)
    for k in range(0, len(j), 6):
        print(j[k:k+6])

in_file.close()
root@PC1:/home/test# cat a.fasta                                   ## 测试fasta文件
>gene1 myc
AGCTGCCTAAGC
GGCATAGCTAATCG
>gene2 jun
ACCGAATCGGAGCGATG
GGCATTAAAGATCTAGCT
>gene3 malat1
AGGCTAGCGAG
GCGCGAG
GATTAGGCG
root@PC1:/home/test# python test.py                               ## 执行程序
>gene1 myc
GCTTAG
GCAGCT
CGATTA
GCTATG
CC
>gene2 jun
CATCGC
TCCGAT
TCGGTA
GCTAGA
TCTTTA
ATGCC
>gene3 malat1
CTCGCT
AGCCTC
TCGCGC
CGCCTA
ATC

 

参考：https://www.jianshu.com/p/5ee54bea4cb0