python 中实现将fasta文件中碱基以每行指定数目输出
作者：互联网
001、测试数据
[root@PC1 test2]# ls
a.fa test.py
[root@PC1 test2]# cat a.fa ## 测试数据
>OR4F5_ENSG00000186092_ENST00000641515_61_1038_2618
CCCAGATCTCTTCAGTTTTTATGCCTCATTCTGTGAAAATTGCTGTAGTCTCTTCCAGTTATGAAGAAGGTAACTGCAGAGGCTATTTCCTGGAATGAATCAACGAGTGAAACGAATAACTCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTT
>OR4F29_ENSG00000284733_ENST00000426406_20_955_995
AGCCCAGTTGGCTGGACCAATGGATGGAGAGAATCACTCAGTGGTATCTGAGTTTTTGTTTCTGGGACTCACTCATTCATGGGAGATCCAGCTCCTCCTCCTAGTGTTTTCCTCTGTGCTCTATGTGGCAAGCATTACTGGAAACATCCTCATTGTGTTTTCTGTGACCACTGACCCTCACTTAC
[root@PC1 test2]# cat test.py ## 转换脚本
#!/usr/bin/python
dict1 = {}
in_file = open("a.fa", "r")
out_file = open("result.fa", "w")
for i in in_file:
i = i.strip()
if i.startswith(">"):
key = i
dict1[key] = ""
else:
dict1[key] += i
len_perline = 20 ## 指定每行的碱基数目
for key, val in dict1.items():
out_file.write(key + "\n")
while len(val) > len_perline:
out_file.write(val[:len_perline] + "\n")
val = val[len_perline:]
out_file.write(val + "\n")
in_file.close()
out_file.close()
[root@PC1 test2]# python test.py ## 执行程序 [root@PC1 test2]# ls a.fa result.fa test.py [root@PC1 test2]# cat result.fa ## 查看结果 >OR4F5_ENSG00000186092_ENST00000641515_61_1038_2618 CCCAGATCTCTTCAGTTTTT ATGCCTCATTCTGTGAAAAT TGCTGTAGTCTCTTCCAGTT ATGAAGAAGGTAACTGCAGA GGCTATTTCCTGGAATGAAT CAACGAGTGAAACGAATAAC TCTATGGTGACTGAATTCAT TTTTCTGGGTCTCTCTGATT CTCAGGAACTCCAGACCTTC CTATTTATGTTGTTTTTT >OR4F29_ENSG00000284733_ENST00000426406_20_955_995 AGCCCAGTTGGCTGGACCAA TGGATGGAGAGAATCACTCA GTGGTATCTGAGTTTTTGTT TCTGGGACTCACTCATTCAT GGGAGATCCAGCTCCTCCTC CTAGTGTTTTCCTCTGTGCT CTATGTGGCAAGCATTACTG GAAACATCCTCATTGTGTTT TCTGTGACCACTGACCCTCA CTTAC
标签：test2,val,python,碱基,fa,file,PC1,fasta,root 来源： https://www.cnblogs.com/liujiaxin2018/p/16353631.html