python中输出fasta文件中碱基的互补序列

 

001、

root@PC1:/home/test# 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.startswith(">"):
        key = i
        dict1[key] = []
    else:
        temp = i.replace("A","t").replace("T","a").replace("C","g").replace("G","c").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
TCGACGGATTCG
CCGTATCGATTAGC
>gene2 jun
TGGCTTAGCCTCGCTAC
CCGTAATTTCTAGATCGA
>gene3 malat1
TCCGATCGCTC
CGCGCTC
CTAATCCGC

 

002、同时指定输出每行的碱基数目

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

in_file = open("a.fasta", "r")
dict1 = {}
for i in in_file:
    i = i.strip()
    if i.startswith(">"):
        key = i
        dict1[key] = []
    else:
        temp = i.replace("A","t").replace("T","a").replace("C","g").replace("G","c").upper()
        dict1[key].append(temp)

for i,j in dict1.items():
    print(i)
    j = "".join(j)
    for k in range(0, len(j), 10):
        print(j[k:k+10])
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
TCGACGGATT
CGCCGTATCG
ATTAGC
>gene2 jun
TGGCTTAGCC
TCGCTACCCG
TAATTTCTAG
ATCGA
>gene3 malat1
TCCGATCGCT
CCGCGCTCCT
AATCCGC