儿童天赋脚本

#!/usr/bin/python
#coding:utf-8
__author__ = 'similarface'
import time
import sys,datetime,re,subprocess
#发送邮件
from itertools import islice
import commands,optparse,os,xlrd
import sys
import smtplib
from email.mime.text import MIMEText
mailto_list=["xx@qq.com",'xx@23mofang.com','xx@23mofang.com']
#设置服务器
mail_host="smtp.qq.com"
#用户名
mail_user="xx@23mofang.com"
#口令
mail_pass="xx"
#发件箱的后缀
mail_postfix="qq.com"

def send_mail(to_list,sub,content):
    #这里的hello可以任意设置，收到信后，将按照设置显示
    me="数据部运行消息"+"<"+mail_user+"@"+mail_postfix+">"
    #创建一个实例，这里设置为html格式邮件
    msg = MIMEText(content,_subtype='html',_charset='UTF-8')
    #设置主题
    msg['Subject'] = sub
    msg['From'] = me
    msg['To'] = ";".join(to_list)
    try:
        s = smtplib.SMTP()
        #连接smtp服务器
        s.connect(mail_host)
        #登陆服务器
        s.login(mail_user,mail_pass)
        #发送邮件
        s.sendmail(me, to_list, msg.as_string())
        s.close()
        return True
    except Exception, e:
        print str(e)
        return False

#basedir
basedir="/data3/childtalent"
#rar原始文件存放目录
rarpath=os.path.join(basedir,"current")
#old原始文件存放目录
oldpath=os.path.join(basedir,"oldrar")
#rar解压缩目录
extractpath=os.path.join(basedir,"extract")
#vcf存放的目录
__resultebase='/data2/vsftp/ertongtianfu/'
#引用对比数据库
__ref=os.path.join(basedir,"db","refAllele.txt")
#命令行
__run=os.path.join(basedir,"run","LDR2Vcf.pl")
#版本文件存放处
versionfile=os.path.join(basedir,"version","version.pid")
#XLS 转的txt的存放目录：
txtoutputdir=os.path.join(basedir,"result")

def unrarPackage(inputPath,outputDir):
    if os.path.exists(inputPath) and inputPath.endswith("rar"):
        (status, output) = commands.getstatusoutput('/usr/local/bin/rar x '+inputPath+' '+outputDir)
        if status!=0:
            print(output)
            return False
        else:
            return True

def getXlsxFromunrarDic(unrardir):
    '''
    获取xlsx文件
    :param unrardir:
    :return:
    '''
    for sondir in os.listdir(unrardir):
        if os.path.isdir(os.path.join(unrardir,sondir)):
            for file in os.listdir(os.path.join(unrardir,sondir)):
                if file.endswith("xlsx"):
                    return os.path.join(unrardir,sondir,file)

def readExcelConvertoTxt(excel,txtPath):
    try:
        f=open(txtPath,'w')
        data=xlrd.open_workbook(excel)
        table=data.sheet_by_name(u'ET样品')
        #行
        nrows = table.nrows
        #列
        ncols = table.ncols
        for i in range(nrows):
            if i==0:
                headerline=['Sample']
                for i in table.row_values(i):
                    if i.startswith("rs"):
                        headerline.append(i)
                f.writelines('	'.join(headerline)+'
')
            elif i==1:
                pass
            else:
                f.writelines('	'.join([ table.row_values(i)[j]  for j in range(ncols) if j not in[0,2,3]])+'
')
                print([ table.row_values(i)[j]  for j in range(ncols) if j not in[0,2,3]])
        f.close()
    except Exception,e:
        print(e)


def getDateFlag():
    '''
    获取日期时间字符串
    :return:20000101
    '''
    return str(time.strftime("%Y%m%d"))

def getDateDetailFlag():
    '''
    获取日期时间字符串
    :return:20000101
    '''
    return str(time.strftime("%Y%m%d-%H:%M:%S"))

def getVersionFromFile(vfile):
    '''
    获取版本信息
    :param vfile:
    :return:
    '''
    try:
        with open(vfile,'r') as v:
            for line in islice(v,0,1):
                result=str(line.split('	')[0])
        if result==None or result=="":
            return 0
        else:
            return int(result)
    except Exception,e:
        return 0

def getOutPutTxtFile():
    return os.path.join(txtoutputdir,getDateFlag()+"GeneResult."+str(getVersionFromFile(versionfile))+'.txt')

def writeVersionFrom(file):
    '''
    书写版本到文件
    :param file:
    :return:
    '''
    version=getVersionFromFile(file)
    contextlist=[]
    try:
        with open(file,'r') as v:
            context=v.read()
        contextlist=context.split('
')
        contextlist.insert(0,str(version+1)+"	"+str(time.strftime("%Y-%m-%d %H:%M:%S")))
    except Exception,e:
        contextlist.insert(0,str(version+1)+"	"+str(time.strftime("%Y-%m-%d %H:%M:%S")))
    with open(file,'w') as v:
        v.write('
'.join(contextlist))

def txtConvertToVcf(txtPath):
        '''
        将txt文本转换成vcf
        '''
        resultpath=getResultDirWithTxt()
        if os.path.exists(txtPath) and os.path.isfile(txtPath):
            print('源TXT:'+txtPath)
            print('源TXT行数:'+getTxtLineSum(txtPath))
            runStr='perl '+__run+' '+txtPath+' '+__ref +' '+resultpath
            print(runStr)
            child = subprocess.Popen(runStr,shell=True)
            isSuccess=child.wait()
            if isSuccess:
                print('txt转换成vcf失败!')
                return 0
            else:
                print('TXT转换成VCF成功!')
                print('VCF文件生成路径:'+resultpath)
                print('VCF生成数:'+getVcfSum(resultpath))
                return getVcfSum(resultpath)
        else:
            print('源TXT文件不存在')
            print('VCF生成数:0')
            return 0

def getTxtLineSum(txtPath):
        '''
        获取运行文件的行数
        txtPath=文件的行数
        返回：文件的行数  不存在返回0行
        '''
        count=1
        if os.path.exists(txtPath) and os.path.isfile(txtPath):
            count = len(open(txtPath,'rU').readlines())
        return str(count-1)



def getResultDirWithTxt():
        #基础文件路径
        basepath=__resultebase
        #运行结果的存放文件夹
        try:
            #获取文件中的日期作为输出目录的标示
            flag=re.match('(^d{8})GeneResult*',getOutPutTxtFile()).group(1)
            print("flag",flag)
            path=os.path.join(basepath,flag)
        except Exception,e:
            path=getResultDirWithCurrData()
        #path=os.path.join(basepath,self.__runid)
        if os.path.exists(path):# and (os.path.isdir(path) or os.path.isfile(path):
            print('输出的文件夹已经存在, 存在的文件夹中有文件数:'+getVcfSum(path))
            print("请选择是否继续y/n?")
            goon=raw_input()
            while 1:
                if goon=='y' or goon=='Y':
                    return path
                if goon=='N' or goon=='n':
                    sys.exit(-1)
                print "请输入y/n ?",
                goon=raw_input()
        else:
            os.mkdir(path)
        return path

def getResultDirWithCurrData():
        #基础文件路径
        basepath=__resultebase
        #运行结果的存放文件夹
        path=os.path.join(basepath,getDateFlag())
        return path


def getVcfSum(path):
    '''
    获取vcf生产的个数
    '''
    "*.vcf"
    j=0
    for i in os.listdir(path):
       if i.endswith("vcf"):
           j=j+1
    return str(j)


def getFileSum(dir):
    '''
    获取vcf生产的个数
    '''
    "*.vcf"
    j=0
    for i in os.listdir(dir):
        j=j+1
    return str(j)

if __name__=='__main__':
    usage = "ertongtianfu[ -f <rar>]"
    opter=optparse.OptionParser(usage)
    opter.add_option("-f","--file",action="store",dest="rar",help="append rar file")
    opt,args=opter.parse_args()
    rarfile=opt.rar
    if rarfile==None or rarfile=="":
        for file in os.listdir(rarpath):
            if file.endswith("rar"):
                rarfile=os.path.join(rarpath,file)
                break
        if rarfile==None or rarfile=="":
            opter.print_help()
            sys.exit(0)
    #解压缩文件
    print("清理解压文件")
    (status, output) = commands.getstatusoutput('rm -rf '+extractpath+"/*")
    if status!=0:
        print(output)
    print('解压缩文件')
    unrarPackage(rarfile,extractpath)
    #EXCEL文件
    print("读取EXCEL文件")
    excelfile=getXlsxFromunrarDic(extractpath)
    #写入批次文件
    print("写入批次文件")
    writeVersionFrom(versionfile)
    txtPath=getOutPutTxtFile()
    #EXCEL到txt文件
    print("EXCEL到txt文件")
    readExcelConvertoTxt(excelfile,txtPath)
    #txt到vcf
    print("txt到vcf")
    vcfnum=txtConvertToVcf(txtPath)
    #清理解压文件
    print("清理解压文件")
    (status, output) = commands.getstatusoutput('rm -rf '+extractpath+"/*")
    if status!=0:
        print(output)

    (status, output) = commands.getstatusoutput('mv '+rarpath+"/* " +oldpath+"/")
    if status!=0:
        print(output)
    print(getVersionFromFile(versionfile),vcfnum,getDateFlag(),rarfile,getTxtLineSum(txtPath))
    mailcontext="批次:"+str(getVersionFromFile(versionfile))+"</br>样本个数:"+str(vcfnum)+"<br/>标志位:"+str(getDateDetailFlag())+"<br/>原始文件:"+os.path.basename(rarfile)+"<br/>获取路" 
                                                                                                                                              "径:ftp://192.168.30.252/ertongtianfu/"+getDateFlag()
    send_mail(mailto_list,"儿童天赋分析结果",mailcontext)