以下代码均为个人原创，如有疑问，欢迎交流。新浪微博：拾毅者

本节内容：

• pssm生成
• pssm简化
• 标准的pssm构建
• 滑动pssm生成

在基于蛋白质序列的相关预測中。使用PSSM打分矩阵会得将预測效果大大提高，同一时候，假设使用滑动的PSSM，效果又会进一步提高。这里主要以分享代码为主，以下介绍下PSSM从生成到处理的全过程。

1.PSSM的生成

PSSM的生成有多种方式，这里使用的psiblast软件。ncbi-blast-2.2.28+/bin/psiblast。下载地址：http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews#1 用法。输入一个序列，加上相关參数，直接输出PSSM文件

代码

#一个命令函数，依据pdb文件。使用blast生成pssm文件
def command_pssm(content, output_file,pssm_file):os.system('/ifs/share/lib/blast/ncbi-blast-2.2.28+/bin/psiblast \-query %s \-db /ifs/data/database/blast_data/nr \-num_iterations 3 \-out %s \-out_ascii_pssm %s &' %(content, output_file,pssm_file))

上面是运行的命令，封装成函数，以下为实际代码：

#对每一个序列进行PSSM打分
def pssm(proseq,outdir):inputfile = open(proseq,'r')content = ''input_file = ''output_file = ''pssm_file = ''chain_name = []for eachline in inputfile:if '>' in eachline:if len(content):temp_file = open(outdir + '/fasta/' + chain_name,'w')temp_file.write(content)input_file = outdir + '/fasta/' + chain_nameoutput_file = outdir + '/' + chain_name + '.out'pssm_file = outdir + '/' + chain_name + '.pssm'                command_pssm(input_file, output_file,pssm_file)temp_file.closecontent = ''chain_name = eachline[1:5] + eachline[6:7]content +=  ''.join(eachline)#print content#print chain_nameif len(content):temp_file = open(outdir + '/fasta/' + chain_name,'w')temp_file.write(content)input_file = outdir + '/fasta/' + chain_nameoutput_file = outdir + '/' + chain_name + '.out'pssm_file = outdir + '/' + chain_name + '.pssm'command_pssm(input_file, output_file,pssm_file)  temp_file.closeinputfile.close()       

測试用例：

'''
#生成pssm文件，迭代次数为3
proseq = '/ifs/home/liudiwei/experiment/step2/data/protein.seq'
outdir = '/ifs/home/liudiwei/experiment/step2/pssm'
pssm(proseq,outdir)
'''

PSSM输出例子：

2.简化PSSM数据

通常我们须要的仅仅是前面的20列

以下通过代码来实现上面的功能：

#格式化pssm每行数据
def formateachline(eachline):col = eachline[0:5].strip()col += '\t' + eachline[5:8].strip()    begin = 9 end = begin +3for i in range(20):     begin = beginend = begin + 3col += '\t' + eachline[begin:end].strip()begin = endcol += '\n'return col

简化pssm。仅仅要得到前面的20个氨基酸的打分值

def simplifypssm(pssmdir,newdir):listfile = os.listdir(pssmdir)for eachfile in listfile:with open(pssmdir + '/' + eachfile,'r') as inputpssm:with open(newdir + '/' + eachfile,'w') as outfile:count = 0for eachline in inputpssm:count +=1if count <= 3:continueif not len(eachline.strip()):breakoneline = formateachline(eachline)outfile.write(''.join(oneline))
''' Test example
pssmdir = '/ifs/home/liudiwei/experiment/step2/pssm/oldpssm'
newdir = '/ifs/home/liudiwei/experiment/step2/pssm/newpssm'
simplifypssm(pssmdir, newdir)
'''

3.得到标准的PSSM

通过上面抽取出来的PSSM，以下通过代码来获得一个滑动的PSSM

#标准的pssm,直接依据标准的pssm滑动
def standardPSSM(window_size,pssmdir,outdir):listfile = os.listdir(pssmdir)for eachfile in listfile:outfile = open(outdir + '/' + eachfile, 'w') with open(pssmdir + '/' + eachfile, 'r') as inputf:inputfile = inputf.readlines()for linenum in range(len(inputfile)):content = []first = [];second = [];third=[];last=[]if linenum < window_size/2:for i in range((window_size/2 - linenum)*20):second.append('\t0')if window_size/2 - linenum > 0:countline = window_size - (window_size/2 - linenum)else:countline = window_size  #get needed line countlinetemp = 0for eachline in inputfile:if linetemp < linenum-window_size/2:linetemp += 1continueif linetemp == linenum:thisline = eachline.split('\t')for j in range(0,2):if j>0:first.append('\t')first.append(thisline[j].strip())if countline > 0:oneline = eachline.split('\t')for j in range(2,len(oneline)):third.append('\t' + oneline[j].strip())countline -=1else:breaklinetemp += 1while countline:for i in range(20):last.append('\t0')countline -=1content += first + second + third + lastoutfile.write(''.join(content) + '\n')outfile.close()'''Test example
pssmdir = '/ifs/home/liudiwei/experiment/step2/pssm/newpssm'
newdir = '/ifs/home/liudiwei/experiment/step2/pssm/standardpssm'
window_size = 5
standardPSSM(window_size,pssmdir, newdir)
'''

4.依据滑动窗体求出滑动的PSSM

#依据窗体大小,计算出滑动后的20个氨基酸打分值
def computedPSSM(window_size,pssmdir,outdir):listfile = os.listdir(pssmdir)for eachfile in listfile:outfile = open(outdir + '/' + eachfile, 'w') with open(pssmdir + '/' + eachfile, 'r') as inputf:inputfile = inputf.readlines()for linenum in range(len(inputfile)):content = []first = [];second = []if window_size/2 - linenum > 0:countline = window_size - (window_size/2 - linenum)else:countline = window_size  #get needed line countlinetemp = 0for eachline in inputfile:if linetemp < linenum-window_size/2:linetemp += 1continueif linetemp == linenum:thisline = eachline.split('\t')for j in range(0,2):if j>0:first.append('\t')first.append(thisline[j].strip())if countline > 0: oneline = eachline.split('\t')[2:len(eachline)]tline = []for i in range(len(oneline)):tline.append(int(oneline[i]))if len(second)==0:second += tlineelse:second = list(map(lambda x: x[0]+x[1], zip(second, tline)))countline -=1 else:break linetemp += 1 format_second = []for i in range(len(second)):format_second.append('\t' + str(second[i]))content += first + format_second outfile.write(''.join(content) + '\n')outfile.close()
'''
pssmdir = '/ifs/home/liudiwei/experiment/step2/pssm/newpssm'
newdir = '/ifs/home/liudiwei/experiment/step2/pssm/computedpssm'
window_size = 5
computedPSSM(window_size,pssmdir, newdir)
'''

平滑的PSSM，仅仅是pssmdir不同，直接调用standardPSSM函数

def smoothedPSSM(window_size,pssmdir,outdir):standardPSSM(window_size,pssmdir, outdir)'''Test example
pssmdir = '/ifs/home/liudiwei/experiment/step2/pssm/computedpssm'
newdir = '/ifs/home/liudiwei/experiment/step2/pssm/smoothedpssm'
window_size = 5
smoothedPSSM(window_size,pssmdir,newdir)
'''

最后得到的是一个滑动的PSSM矩阵，特征的维数随窗体的大小逐渐增减。