Python 序列中的计数模式

我在文本文件中有如下顺序

import re

infile=open("seq.fasta",'r')

out=open("results.csv",'w')
pattern=re.compile(r"(P[A-Z]{2}P)")
for line in infile:
    line = line.strip("\n")
    if line.startswith('>'):
        name=line
    else:
        s = re.findall(pattern,line)
    print '%s:%s' %(name,s)
    out.write('%s:\t%s\n' %(name,s))

> P1

MPPRRSIVEVKVLDVQKRRRVPNKYVYVIIRVTWSGATEAYRRYSKFFDLQMLDKFP MEGGQKDPKQRIIPFLpgILFRSHIRDVAVKRIPIDEYCPYISQCDEVFETRPELDLNPLNPLNPLNPLNPLNPLNPLVVQVQVVADQQQESSEISLZWWWWVSTAEQWVPATCLEGQDGVQDFEFGFLQPEEEKYPTIQQIDLQEDEKWKKKYKKKKKWKKKWKKWKKKKYGPLNPLNPLNPLNPLNPLNPLNPLNPLNPLNPLNPLNPLNPLNPLNPLNPLNPLNPLNPDGVSRHQNAMGREKELLNNQRDGRFEGRLVPDVKQRSPKMRQRPPPRRDMTIPRGLNL

> P2

MaevrkftkrkPgTaaelVgLekKlveplDyenvTdLdLmFpMedicinesvigrrTvTvTvPedekRaqLvKecTvHvNyKye DFSGFRMlPcKsLpKgKgKgKgKgKgKgKgKgKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKfKENIMASLERSMHPELMKYGRETEQLNKLSRGDGRQNLFSFDSEVQRLDFSGIEPDVKPFE ekcnkrfmvnchdltfnillghdnakgpptinveffinlalfdvknnckyisdfdln ppsvremlwgtstqlsndgnakgfspeshlighgaesqlcyikgiftnppeifvr

> P3

GDDSEWLPVDQKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK根据VVKKKVGKDTNVMLVALAAKCLTGLAVGLKKKKGQYAG HVVPTILEKKKKKKQVQQQQAIDAIFLTTTLQNISEDVLDNKNPTIKQQQTSLFI ARSFRCTSSTLPKLKPFCAALLKINDSAPEVRDAAFEGTALLKVQGEKSVNPFLA

在这些序列中总共有100个序列，我使用python脚本搜索了一个感兴趣的模式，如下所示

import re

infile=open("seq.fasta",'r')

out=open("results.csv",'w')
pattern=re.compile(r"(P[A-Z]{2}P)")
for line in infile:
    line = line.strip("\n")
    if line.startswith('>'):
        name=line
    else:
        s = re.findall(pattern,line)
    print '%s:%s' %(name,s)
    out.write('%s:\t%s\n' %(name,s))

这个脚本运行得很好，它给了我想要的模式…现在我想计算脚本中出现的每个序列中感兴趣的模式，如下所示

import re

infile=open("seq.fasta",'r')

out=open("results.csv",'w')
pattern=re.compile(r"(P[A-Z]{2}P)")
for line in infile:
    line = line.strip("\n")
    if line.startswith('>'):
        name=line
    else:
        s = re.findall(pattern,line)
    print '%s:%s' %(name,s)
    out.write('%s:\t%s\n' %(name,s))

>

p1:PGCP

>

p1:PHCP，PKCP。诸如此类

但我想发布如下>

p1:1

>

p1:2

---

有谁能告诉我如何使用python实现这一点吗

findall

方法返回匹配字符串的列表。因此，您可以在代码中使用

len（s）

，而不是

s

out.write('%s:\t%s\n' %(name,len(s)))

---

findall

方法返回匹配字符串的列表。因此，您可以在代码中使用

len（s）

，而不是

s

out.write('%s:\t%s\n' %(name,len(s)))