python 中 实现将fasta文件碱基按照每行指定数目输出

 

001、

(base) root@PC1:/home/test2# ls
a.fasta  test.py
(base) root@PC1:/home/test2# cat a.fasta                      ## 测试数据
>scaffold_1
CCCGGGTAAAACGGGTCTTCAAGAAAACGCTCCTCCGTTAATGCCGGCCGATTCAAATAA
CGCTGATTCTGATTCAGGATATACAATCTGACATGATGAACAGGTTTTCCAATTGGAATC
>scaffold_2
CACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCGATAAATGGATCACAGGTT
AAGTTCACCGCATCCTGCGGCGACACCTGTGTGGCCTGCGTCGTGCAGGCCCTAGTTTGA
CTGACTACGCACATCGCTGTGCGATTTATAAAAATGAATTAACAGGTACGTTTTGTCTTG
>scaffold_3
TTGATCCAGTGGCTCCGGTTACTCCAGTTGATCCTGTTGCGCCTGTTGCTCCAGTTTCTC
CGGTTGGTCCGGTTGATCCGGTTGCA
>scaffold_4
CCTGAGCCAGGATCAAACTCTCCGATAAATGGATCACAGGTTAAGTTCACCGCATCCTGC
GGCGACACCTGTGAGGTACGTTTTGTCTTGT
(base) root@PC1:/home/test2# cat test.py                      ## 测试脚本
#!/usr/bin/python
in_file = open("a.fasta", "r")
out_file = open("result.txt", "w")
dict1 = dict()

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

step = 40                                                      ## 此处指定每行的碱基数目
for i,j in dict1.items():
    out_file.write(i + "\n")
    while len(j) > step:
        out_file.write(j[:step] + "\n")
        j = j[step:]
    out_file.write(j[::] + "\n")

in_file.close()
out_file.close()
(base) root@PC1:/home/test2# python test.py                   ## 执行程序
(base) root@PC1:/home/test2# ls
a.fasta  result.txt  test.py
(base) root@PC1:/home/test2# cat result.txt                   ## 查看结果
>scaffold_1
CCCGGGTAAAACGGGTCTTCAAGAAAACGCTCCTCCGTTA
ATGCCGGCCGATTCAAATAACGCTGATTCTGATTCAGGAT
ATACAATCTGACATGATGAACAGGTTTTCCAATTGGAATC
>scaffold_2
CACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTC
CGATAAATGGATCACAGGTTAAGTTCACCGCATCCTGCGG
CGACACCTGTGTGGCCTGCGTCGTGCAGGCCCTAGTTTGA
CTGACTACGCACATCGCTGTGCGATTTATAAAAATGAATT
AACAGGTACGTTTTGTCTTG
>scaffold_3
TTGATCCAGTGGCTCCGGTTACTCCAGTTGATCCTGTTGC
GCCTGTTGCTCCAGTTTCTCCGGTTGGTCCGGTTGATCCG
GTTGCA
>scaffold_4
CCTGAGCCAGGATCAAACTCTCCGATAAATGGATCACAGG
TTAAGTTCACCGCATCCTGCGGCGACACCTGTGAGGTACG
TTTTGTCTTGT

 

参考：https://mp.weixin.qq.com/s?__biz=MzIxNzc1Mzk3NQ==&mid=2247491492&idx=1&sn=d9bfd396369b802700ef764d8174669d&chksm=97f5afbca08226aa255d2ee747a179a1e13e9160baf87b4186f871e396e8b86c826a5ca51ef4&scene=178&cur_album_id=2403674812188688386#rd