正则表达式Python变量

Question

我有这样的数据:

>Px016979
MSPWMKKVFLQCMPKLLMMRRTKYSLPDYDDTFVSNGYTNELEMSRDSLT
DAFGNSKEDSGDYRKSPAPEDDMVGAGAYQRPSVTESENMLPRHLSPEVA
AALQSVRFIAQHIKDADKDNEVVEDWKFMSMVLDRFFLWLFTIACFVGTF
GIIFQSPSLYDTRVPVDQQISSIPMRKNNFFYPKDIETIGIIS
>Px016980
MQFIKKVLLIALTLSGAMGISREKRGLIFPPTSLYGTFLAIAVPIDIPDK
NVFVSYNFESNYSTLNNITEIDEVLFPNLPVVTARHSRSITRELAYTVLE
TKFKEHGLGGRECLLRNICEAAETPLHHNGLLGHIMHIVFTPSSSAEEGL
DDEYYEAEASGRAGSCARYEELCPVGLFDLITRIVEFKHT
>Px002185
MLSPSVAIKVQVLYIGKVRISQRKVPDTLIDDALVKFVHHEAEKVKANML
RRHSLLSSTGTSIYSSESAENLNEDKTKTDTSEHNIFLMMLLRAHCEAKQ
LRHVHDTAENRTEFLNQYLGGSTIFMKAKRSLSSGFDQLLKRKSSRDEGS
GLVLPVKKVT
>Px006321
MFPGRTIGIMITASHNLEPDNGVKLVDPDGEMLDGSWEEIATRMANVRYL
PMSLITKFLVNSYY

我想要做的是,如果我有数字> Px016979或我可以得到它下面的数据.像这样:

>Px016979
MSPWMKKVFLQCMPKLLMMRRTKYSLPDYDDTFVSNGYTNELEMSRDSLT
DAFGNSKEDSGDYRKSPAPEDDMVGAGAYQRPSVTESENMLPRHLSPEVA
AALQSVRFIAQHIKDADKDNEVVEDWKFMSMVLDRFFLWLFTIACFVGTF
GIIFQSPSLYDTRVPVDQQISSIPMRKNNFFYPKDIETIGIIS

我是Python新手.

#coding:utf-8
import os,re


a =   """ 
    >Px016979 
    MSPWMKKVFLQCMPKLLMMRRTKYSLPDYDDTFVSNGYTNELEMSRDSLT 
    DAFGNSKEDSGDYRKSPAPEDDMVGAGAYQRPSVTESENMLPRHLSPEVA 
    AALQSVRFIAQHIKDADKDNEVVEDWKFMSMVLDRFFLWLFTIACFVGTF 
    GIIFQSPSLYDTRVPVDQQISSIPMRKNNFFYPKDIETIGIIS 
    >Px016980 
    MQFIKKVLLIALTLSGAMGISREKRGLIFPPTSLYGTFLAIAVPIDIPDK 
    NVFVSYNFESNYSTLNNITEIDEVLFPNLPVVTARHSRSITRELAYTVLE 
    TKFKEHGLGGRECLLRNICEAAETPLHHNGLLGHIMHIVFTPSSSAEEGL 
    DDEYYEAEASGRAGSCARYEELCPVGLFDLITRIVEFKHT"
    >Px002185
    MLSPSVAIKVQVLYIGKVRISQRKVPDTLIDDALVKFVHHEAEKVKANML
    RRHSLLSSTGTSIYSSESAENLNEDKTKTDTSEHNIFLMMLLRAHCEAKQ
    LRHVHDTAENRTEFLNQYLGGSTIFMKAKRSLSSGFDQLLKRKSSRDEGS
    GLVLPVKKVT
    >Px006321
    MFPGRTIGIMITASHNLEPDNGVKLVDPDGEMLDGSWEEIATRMANVRYL
    PMSLITKFLVNSYY

    """

  b = '>Px016979'


  matchbj = re.match( r'$b(.*?)>',a,re.M|re.I)

  print matchbj.group()

我的代码无法正常工作.我有两个问题:

1. 我认为我的数据有回车,所以我的代码无法正常工作.

2. 我不知道如何在Python正则表达式中使用变量.如果我写re.match( r'>Px016797(.*?)>',a,re.M|re.I)它可以工作,但我需要使用变量.

谢谢.

Answer 1

看起来您的数据是带有蛋白质序列的FASTA文件.因此,您应该考虑安装BioPython而不是使用正则表达式.这是一个专门用于生物信息学使用和研究的图书馆.

Biopython的目标是通过创建高质量,可重复使用的模块和类,使Python尽可能容易地用于生物信息学.Biopython功能包括各种生物信息学文件格式(BLAST,Clustalw,FASTA,Genbank等)的解析器,访问在线服务(NCBI,Expasy,...),与常见和不常见程序的接口(Clustalw, DSSP,MSMS ...),标准序列类,各种聚类模块,KD树数据结构等甚至文档.

使用BioPython,您将通过以下方式从FASTA文件中提取给定标识符的序列:

from Bio import SeqIO

input_file = r'C:\path\to\proteins.fasta'
record_id = 'Px016979'
record_dict = SeqIO.to_dict(SeqIO.parse(input_file, 'fasta'))
record =  record_dict[record_id]
sequence = str(record.seq)

print sequence