#!/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('\t'.join(headerline)+'\n')
elif i==1:
pass
else:
f.writelines('\t'.join([ table.row_values(i)[j] for j in range(ncols) if j not in[0,2,3]])+'\n')
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('\t')[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('\n')
contextlist.insert(0,str(version+1)+"\t"+str(time.strftime("%Y-%m-%d %H:%M:%S")))
except Exception,e:
contextlist.insert(0,str(version+1)+"\t"+str(time.strftime("%Y-%m-%d %H:%M:%S")))
with open(file,'w') as v:
v.write('\n'.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)
