python中 pysam包FastxFile函数

 

001、读取fasta文件

root@PC1:/home/test# ls
a.fasta
root@PC1:/home/test# cat a.fasta                         ## 测试数据
>Rosalind_1
ATCCAGCT
>Rosalind_2
GGGCAACT
>Rosalind_3
ATGGATCT
>Rosalind_4
AAGCAACC
>Rosalind_5
TTGGAACT
>Rosalind_6
ATGCCATT
>Rosalind_7
ATGGCACT
root@PC1:/home/test# python                                       ## 启动python
Python 3.10.4 (main, Mar 31 2022, 08:41:55) [GCC 7.5.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysam                                                  ## 导入pysam包
>>> in_file = pysam.FastxFile("a.fasta")                          ## 读取数据，生成可迭代对象
>>> for i in in_file:
...     print(i)
...
>Rosalind_1
ATCCAGCT
>Rosalind_2
GGGCAACT
>Rosalind_3
ATGGATCT
>Rosalind_4
AAGCAACC
>Rosalind_5
TTGGAACT
>Rosalind_6
ATGCCATT
>Rosalind_7
ATGGCACT

 

>>> in_file = pysam.FastxFile("a.fasta")
>>> for i in in_file:
...     print(i.name)                     ## 输出scaffold
...
Rosalind_1
Rosalind_2
Rosalind_3
Rosalind_4
Rosalind_5
Rosalind_6
Rosalind_7
>>> in_file = pysam.FastxFile("a.fasta")
>>> for i in in_file:
...     print(i.sequence)                ## 输出序列
...
ATCCAGCT
GGGCAACT
ATGGATCT
AAGCAACC
TTGGAACT
ATGCCATT
ATGGCACT

 

002、

(base) root@PC1:/home/test# ls
a.fasta  b.fasta
(base) root@PC1:/home/test# cat b.fasta                        ## 测试fasta文件
>Rosalind_1
ATCCAGCT
ATCCAGCT
TTTTT
>Rosalind_2
GGGCAACT
GGGCAACT
GGGCAACT
>Rosalind_3
ATGGATCT
ATGGATCT
ATGGATCT
(base) root@PC1:/home/test# python                                   ## 启动python
Python 3.10.4 (main, Mar 31 2022, 08:41:55) [GCC 7.5.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysam                                                     ## 导入pysam包                          
>>> in_file = pysam.FastxFile("b.fasta")
>>> for i in in_file:
...     print(i)                                               ## 将多行序列合并为一行
...
>Rosalind_1
ATCCAGCTATCCAGCTTTTTT
>Rosalind_2
GGGCAACTGGGCAACTGGGCAACT
>Rosalind_3
ATGGATCTATGGATCTATGGATCT

 

参考：https://mp.weixin.qq.com/s?__biz=MzIxMjQxMDYxNA==&mid=2247484172&idx=1&sn=d8dec9ae5ffea81ef02e8f0d7ea4672b&chksm=9747ca95a030438313f483f6c62c9c32551e23682f98be6868edf423ea88180165e21c5dedc8&scene=178&cur_album_id=1635727573621997580#rd