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web_crawler_UniProtKB20180316 - database.py
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web_crawler_UniProtKB20180316 - database.py
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#coding=utf-8
#################################################################################################################
#How it works：
#Import gene names by csv file, then search Uniprot database, matching accession ID and GO annotation, and finally output as xls file.
#6 parameters：
#1. workpath; 2. geneID csv file; 3. output result file; 4. output mismatch file; 5. choose a database.
#Note:
#1. all geneID in one column in csv file;
#2. there may be mismatch accessionID when using gene symbol ID for searching. the 2nd column of result file is geneID from database,
# which is used for proofing ID matching.
#3. python2.7.
#4. model: pyExcelerator。
#Version: Web_Crawler20180316; select GO database.
#author：[email protected]
#################################################################################################################
import urllib
import re
import socket
import os
import time
from pyExcelerator import *
workspace = 'C:\\Users\\huangzhihao\\Desktop'
GOdatabase = '.*?'
inputfile = 'gene.csv'
outputfile = 'gene_annotation_d.xls'
annot_com = 'gene_annotationcomplement_d.xls'
genemiss = 'gene_annotation_miss_d.txt'
starttime = time.asctime(time.localtime(time.time()))
os.chdir(workspace)
def getHtml(url):
page = urllib.urlopen(url)
html = page.read()
return html
def gettitle(html):
reg = r'<title>.*?</title>'
titre = re.compile(reg)
titl = re.findall(titre,html)
titlist = re.match(r'<title>(.*?)\ -\ (.*?)\ -\ (.*?)</title>',titl[0])#matching again;
return titlist
def getfunc(html):
ref = r'</script><meta content=.*?</head>'
funre = re.compile(ref)
fun = re.findall(funre,html)
funlist = re.match(r'</script><meta content=\"(.*?)\"(.*?)</head>',fun[0])
return funlist
def getgo(html):
reg = r';\">.*?Source\: '+ GOdatabase +'<'
gore = re.compile(reg)
gol = gore.findall(html)
golistr =[]
for i in range(len(gol)):
if len(gol[i]) < 5000:
golistr.append(gol[i])
else:
break
golist =[]
for i in range(len(golistr)):
go = re.findall(r';\">(.*?)</a>',str(golistr[i]))
if len(go) <500:
golist.append(go[-1])
return golist
with open(inputfile) as a: ##input csv file
geneid = []
for line in a.readlines():
geneid.append(line.strip())
w=Workbook()
ws = w.add_sheet('id')
ws.write(0,0,"GeneID") ##write 5 columns
ws.write(0,1,"GeneID_ac")
ws.write(0,2,"Protein Names")
ws.write(0,3,"function")
database_name = 'alldatabase' if GOdatabase =='.*?' else GOdatabase
ws.write(0,4,"GO_annotation"+"_"+database_name)
missac = []
network = 'The network connection is successful!'
for i in range(len(geneid)):
socket.setdefaulttimeout(30)
try:
htmls = getHtml("http://www.uniprot.org/uniprot/?query=organism%3A%22Homo+sapiens+%28Human%29+%5B9606%5D%22+"+geneid[i]+"&sort=score") #联网搜ac号
ref = r'</script></td></tr></thead><tbody><tr\ id=\".*?\" class=\"\ entry\ selected-row'
accom = re.compile(ref)
plist = re.findall(accom,htmls)
acma = re.match(r'</script></td></tr></thead><tbody><tr\ id=\"(.*?)\" class=\"\ entry\ selected-row',plist[0])
acnumber = acma.group(1)
except:
print geneid[i]+" can't connect Uniprot in 30s, we will connect once again..."
socket.setdefaulttimeout(30)
try:
htmls = getHtml("http://www.uniprot.org/uniprot/?query=organism%3A%22Homo+sapiens+%28Human%29+%5B9606%5D%22+"+geneid[i]+"&sort=score") #联网搜ac号
ref = r'</script></td></tr></thead><tbody><tr\ id=\".*?\" class=\"\ entry\ selected-row'
accom = re.compile(ref)
plist = re.findall(accom,htmls)
acma = re.match(r'</script></td></tr></thead><tbody><tr\ id=\"(.*?)\" class=\"\ entry\ selected-row',plist[0])
acnumber = acma.group(1)
print "reconnection is seccessful!"
except:
print "can't connect the uniprot "+geneid[i]
missac.append(geneid[i]) #mismatch ID was stored in missac
try:
print "connecting the No."+str(i+1)+" gene "+geneid[i]+", please wait..."
html = getHtml("http://www.uniprot.org/uniprot/"+acnumber) #connecting
if len(html) < 1000:
network = 'the network had been broken!' ###special case.unipro html contain mor than 1000 rows. 为什么不直接html == None？因为之前在学校断网自动跳到锐捷验证，有源代码<1000
except:
print geneid[i]+" can't connect web in 30s, we will connect once again..."
socket.setdefaulttimeout(30)
try:
html = getHtml("http://www.uniprot.org/uniprot/"+acnumber)
print "reconnection is seccessful!"
except:
print "can't connect the web-"+geneid[i]
missac.append(geneid[i])
try:
print geneid[i]+" is matching..."
ws.write(i+1,0,geneid[i])
ws.write(i+1,1,''.join(gettitle(html).group(1)))
ws.write(i+1,2,''.join(gettitle(html).group(2)))
ws.write(i+1,3,''.join(getfunc(html).group(1)))
ws.write(i+1,4,'; '.join(getgo(html)))
except:
print "can't match the web"+geneid[1]
print "done"
w.save(outputfile) #3. output file;
####running again for mismatch ID.
geneid = missac
missac = []
z=Workbook()
zs = z.add_sheet('id')
ws.write(0,0,"GeneID")
ws.write(0,1,"GeneID_ac")
ws.write(0,2,"Protein Names")
ws.write(0,3,"function")
ws.write(0,4,"GO_annotation"+"_"+GOdatabase)
for i in range(len(geneid)):
socket.setdefaulttimeout(30)
htmls = getHtml("http://www.uniprot.org/uniprot/?query=organism%3A%22Homo+sapiens+%28Human%29+%5B9606%5D%22+"+geneid[i]+"&sort=score") #联网搜ac号
ref = r'</script></td></tr></thead><tbody><tr\ id=\".*?\" class=\"\ entry\ selected-row'
accom = re.compile(ref)
plist = re.findall(accom,htmls)
acma = re.match(r'</script></td></tr></thead><tbody><tr\ id=\"(.*?)\" class=\"\ entry\ selected-row',plist[0])
acnumber = acma.group(1)
try:
print "connecting the No."+str(i+1)+" gene "+geneid[i]+", please wait..."
html = getHtml("http://www.uniprot.org/uniprot/"+acnumber)
if len(html) < 1000:
network = 'the network had been broken!'
except:
print geneid[i]+" can't connect web in 30s, we will connect once again..."
socket.setdefaulttimeout(30)
try:
html = getHtml("http://www.uniprot.org/uniprot/"+acnumber)
print "reconnection is seccessful!"
except:
print "can't connect the web-"+geneid[i]
missac.append(geneid[i])
try:
print geneid[i]+" is matching..."
zs.write(i+1,0,geneid[i])
zs.write(i+1,1,''.join(gettitle(html).group(1)))
zs.write(i+1,2,''.join(gettitle(html).group(2)))
zs.write(i+1,3,''.join(getfunc(html).group(1)))
zs.write(i+1,4,''.join(getgo(html)))
except:
print "can't match "+geneid[i]
print "done"
z.save(annot_com)
with open(genemiss,'w') as f:
k = ' '.join(i for i in missac);
f.write(k)
endtime = time.asctime(time.localtime(time.time()))
print "\n\n" + network + " The work has been finished.\nStart time: "+str(starttime)+";\nEnd time: "+str(endtime)+"."