项目：fasta 转化 md5库

工作中的一个小的细节记录

将 fasta 用 md5 统一 id

• 拿到 md5 串
• 去除第1行 > 开头的信息
• 将后面行，连接
• 去掉 \n，去2侧的空格 
• 转成纯大写

fasta 串

这个串在 .fasta 文件里是严格行数显示的，所以不用担心一些奇奇怪怪的问题。

>WP_014621546.1 CRISPR-associated endoribonuclease Cas6 [Streptococcus thermophilus] >A0A0A7HF73.1 RecName: Full=CRISPR-associated endoribonuclease Cas6; AltName: Full=Cas6 endoRNase; AltName: Full=Cas6 endoribonuclease [Streptococcus thermophilus] >MBR2538257.1 CRISPR-associated endoribonuclease Cas6 [Streptococcus sp.] >AIZ03603.1 Cas6 protein [Streptococcus thermophilus] >EWM58862.1 CRISPR-associated protein Cas6 [Streptococcus thermophilus TH982] >MBW7829050.1 CRISPR-associated endoribonuclease Cas6 [Streptococcus thermophilus] >MCA6641324.1 CRISPR-associated endoribonuclease Cas6 [Streptococcus thermophilus]
MKKLVFTFKRIDHPAQDLAVKFHGFLMEQLDSDYVDYLHQQQTNPYATKVIQGKENTQWVVHLLTDDHEDKVFMTLLQIK
EVSLNDLPKLSVEKVEIQELGADKLLEIFNSEENQTYFSIIFETPTGFKSQGSYVIFPSMRLIFQSLMQKYGRLVENQPE
IEEDTLDYLSEHSTITNYRLETSYFRVHRQRIPAFRGKLTFKVQGAKTLKAYVKMLLTFGEYSGLGMKTSLGMGGIKLEE
RKD

python 实现

import hashlib
filename = "./P06_000_000_001.fasta"

with open(filename) as f:
    lines = f.readlines()
    res = []
    for line in lines:
        if not line.startswith(">"):
            res.append(line.strip())
    # md5 the res string

    md5 = hashlib.md5()
    md5.update(''.join(res).encode('utf-8'))

    print(md5.hexdigest().upper())

使用 jsw_bio

import jsw_bio as bio

fasta_str = open(filename).read()
bio.ncbi_fasta2md5(fasta_str)

# CCD30D35DEF426190203046E3E71F214