def __init__(self,fd=None):
cmdClass.__init__(self,fd)
if not webqtlConfig.TEXTUI:
self.contents.append("Please send your request to http://robot.genenetwork.org")
return
machineParse = self.data.getvalue('parse')
topic = self.data.getvalue('topic')
if topic:
topic = topic.lower()
if topic == 'tissue':
self.contents.append("%s%s| %s" %("Tissue", ' '*(50-len("Tissue")), "Tissue Abbreviations"))
self.contents.append("%s%s| %s" %("", ' '*50, "(Separated by space, case insensitive)"))
self.contents.append("%s|%s" %('_'*50, '_'*40))
keys = ADMIN_tissue_alias.keys()
keys.sort()
for key in keys:
self.contents.append("%s%s| %s" % (key , ' '*(50-len(key)), string.join(ADMIN_tissue_alias[key], " ")))
self.contents.append("%s|%s" %('_'*50, '_'*40))
else:
pass
else:
self.contents = ["#Use database code table below to access data", "#For machine parse friendly output please use",
"#http://www.genenetwork.org%s%s?cmd=help&parse=machine" % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)]
self.cursor.execute("""(SELECT DBType.Name, DBList.FreezeId, DBList.Code, ProbeSetFreeze.CreateTime as Time
from ProbeSetFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and
DBType.Name = 'ProbeSet' and DBList.FreezeId = ProbeSetFreeze.Id and
ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime ,DBList.Name, DBList.Id)
UNION
(SELECT DBType.Name, DBList.FreezeId, DBList.Code, PublishFreeze.CreateTime as Time
from PublishFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and
DBType.Name = 'Publish' and DBList.FreezeId = PublishFreeze.Id order by
PublishFreeze.CreateTime ,DBList.Name, DBList.Id)
UNION
(SELECT DBType.Name, DBList.FreezeId, DBList.Code, GenoFreeze.CreateTime
from GenoFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and
DBType.Name = 'Geno' and DBList.FreezeId = GenoFreeze.Id order by
GenoFreeze.CreateTime ,DBList.Name, DBList.Id)""" % webqtlConfig.PUBLICTHRESH)
dbs = self.cursor.fetchall()
if machineParse =="machine":
pass
else:
self.contents.append("\n")
self.contents.append("%s%s| %s" %("Database_Name", ' '*(50-len("Database_Name")), "Database_Access_Code_Name"))
self.contents.append("%s|%s" %('_'*50, '_'*40))
for dbInfo in dbs:
self.cursor.execute('SELECT FullName from %sFreeze WHERE Id = %d and public > %d' % (dbInfo[0], dbInfo[1],webqtlConfig.PUBLICTHRESH))
results = self.cursor.fetchall()
if not results:
pass
else:
if machineParse =="machine":
self.contents.append(results[0][0]+ ',' +dbInfo[2])
else:
self.contents.append("%s%s| %s" %(results[0][0], ' '*(50-len(results[0][0])), dbInfo[2]))
self.contents.append("%s|%s" %('_'*50, '_'*40))
def __init__(self,fd):
#example
cmdClass.__init__(self,fd)
self.page = None
self.text = ""
fd.geneName = fd.formdata.getvalue('gene')
fd.returnFmt = fd.formdata.getvalue('format', 'html')
if fd.geneName:
fd.geneName = string.strip(fd.geneName)
fd.refseq = fd.formdata.getvalue('refseq')
if fd.refseq:
fd.refseq = string.strip(fd.refseq)
fd.genbankid = fd.formdata.getvalue('genbankid')
if fd.genbankid:
fd.genbankid = string.strip(fd.genbankid)
fd.geneid = fd.formdata.getvalue('geneid')
if fd.geneid:
fd.geneid = string.strip(fd.geneid)
if 1:
if not (fd.geneName or fd.refseq or fd.genbankid or fd.geneid):
raise "ValueError"
fd.searchAlias = fd.formdata.getvalue('alias')
if fd.searchAlias != '1':
fd.searchAlias = None
self.page = TextSearchPage(fd)
if fd.returnFmt != 'text':
pass
else:
self.text = self.page.output
self.page = None
elif "ValueError":
self.text = "You need to submit a Gene name, a Refseq ID, or a GenBank ID"
else:
self.text = "Error occurs while searching the database"
def __init__(self,fd=None):
cmdClass.__init__(self,fd)
if not webqtlConfig.TEXTUI:
self.contents.append("Please send your request to http://robot.genenetwork.org")
return
if self.accessError:
return
self.error = 0
self.RISet = None
self.chr = None
self.dataset = None
self.strainList = []
try:
self.RISet = self.data.getvalue('riset')
if not self.RISet:
raise ValueError
except:
self.error = 1
self.contents.append('###Example : http://www.genenetwork.org%s%s?cmd=%s&riset=BXD&chr=1' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID))
return
try:
self.format = self.data.getvalue('format')[:3]
except:
self.format = 'row'
try:
self.dataset = reaper.Dataset()
try:
self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno'))
except:
self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet.upper() + '.geno'))
self.strainList = list(self.dataset.prgy)
except:
self.error = 1
#traceback.print_exc()
self.contents.append('###The name of RISet is incorrect')
return
try:
self.chr = self.data.getvalue('chr')
if self.chr:
if self.chr == 'X' or self.chr == 'x':
self.chr = '20'
self.chr = int(self.chr)
except:
pass
self.readGeno()
def __init__(self,fd):
###example = http://www.webqtl.org/cgi-bin/beta/WebQTL?cmd=snp&chr=1&start=0&end=21345677
cmdClass.__init__(self,fd)
self.page = None
prefix, dbId = self.getDBId(self.database)
try:
if not prefix or not dbId:
raise ValueError
self.cursor.execute('SELECT Name from %sFreeze WHERE Id=%d' % (prefix, dbId))
database = self.cursor.fetchall()[0][0]
traitInfos = (database,self.probeset,self.probe)
self.page = ShowTraitPage(fd,traitInfos)
#self = page
except:
print "Database Name Incorrect"
def __init__(self,fd=None):
cmdClass.__init__(self,fd)
if not webqtlConfig.TEXTUI:
self.contents.append("Please send your request to http://robot.genenetwork.org")
return
self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all">%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
if self.accessError:
return
if not self.error:
self.readDB()
else:
self.contents.append(self.example)
self.contents.append(self.accessCode)
def __init__(self,fd=None):
cmdClass.__init__(self,fd)
if not webqtlConfig.TEXTUI:
self.contents.append("Please send your request to http://robot.genenetwork.org")
return
self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
if self.accessError:
return
self.sort = None
self.step = 0.01
self.peak = 1
self.chr = None
self.sort = None
self.returnnumber = 20
if self.error:
self.error = 1
self.contents.append(self.example)
return
else:
try:
self.sort = self.data.getvalue('sort')
if string.lower(self.sort) == 'pos':
self.sort = 'pos'
else:
self.sort = 'lrs'
except:
self.sort = None
try:
self.returnnumber = int(self.data.getvalue('return'))
except:
self.returnnumber = 20
try:
self.chr = self.data.getvalue('chr')
except:
self.chr = None
self.readDB()
def __init__(self,fd=None):
cmdClass.__init__(self,fd)
if not webqtlConfig.TEXTUI:
self.contents.append("Please send your request to http://robot.genenetwork.org")
return
self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
if self.accessError:
return
try:
self.returnnumber = int(self.data.getvalue('return'))
except:
self.returnnumber = None
if self.error:
self.contents.append(self.example)
self.contents.append(self.accessCode)
else:
self.sort = self.data.getvalue('sort')
self.readDB()
def __init__(self,fd=None):
cmdClass.__init__(self,fd)
if not webqtlConfig.TEXTUI:
self.contents.append("Please send your request to http://robot.genenetwork.org")
return
self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
if self.accessError:
return
self.searchDB = self.data.getvalue('searchdb')
if not self.searchDB or self.error:
self.contents.append("###Error: source trait doesn't exist or no target database was given")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
try:
self.returnNumber = int(self.data.getvalue('return'))
except:
self.returnNumber = None
self.sort = self.data.getvalue('sort')
prefix, dbId = self.getDBId(self.database)
if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
RISet = self.getRISet(prefix, dbId)
prefix2, dbId2 = self.getDBId(self.searchDB)
if not prefix2 or not dbId2:
self.contents.append("###Error: target database doesn't exist.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
RISet2 = self.getRISet(prefix2, dbId2)
if RISet2 != RISet:
self.contents.append("###Error: target database has different Mouse InbredSet.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
if not traitdata:
self.contents.append("###Error: source trait doesn't exist.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
StrainNames = []
sourceTrait = []
StrainIds = []
#XZ, Jan 27, 2011: Only the strains that are of the same inbredset are used to calculate correlation.
for item in traitdata:
one_strain_name = item[0]
one_strain_value = item[1]
self.cursor.execute('SELECT Strain.Id from Strain,StrainXRef, InbredSet WHERE Strain.Name="%s" and Strain.Id = StrainXRef.StrainId and StrainXRef.InbredSetId = InbredSet.Id and InbredSet.Name = "%s"' % (one_strain_name, RISet2))
Results = self.cursor.fetchall()
if Results:
StrainIds.append('%d' % Results[0][0])
StrainNames.append( one_strain_name )
sourceTrait.append( one_strain_value )
correlationArray = []
useFastMethod = False
if prefix2 == "ProbeSet":
DatabaseFileName = self.getFileName( target_db_id=dbId2 )
DirectoryList = os.listdir(webqtlConfig.TEXTDIR) ### List of existing text files. Used to check if a text file already exists
if DatabaseFileName in DirectoryList:
useFastMethod = True
if useFastMethod:
datasetFile = open(webqtlConfig.TEXTDIR+DatabaseFileName,'r')
#XZ, 01/08/2009: read the first line
line = datasetFile.readline()
dataset_strains = webqtlUtil.readLineCSV(line)[1:]
#XZ, 01/08/2009: This step is critical. It is necessary for this new method.
_newvals = []
for item in dataset_strains:
if item in StrainNames:
_newvals.append(sourceTrait[StrainNames.index(item)])
else:
_newvals.append('None')
nnCorr = len(_newvals)
for line in datasetFile:
traitdata=webqtlUtil.readLineCSV(line)
traitdataName = traitdata[0]
traitvals = traitdata[1:]
corr,nOverlap = webqtlUtil.calCorrelationText(traitvals,_newvals,nnCorr)
traitinfo = [traitdataName,corr,nOverlap]
correlationArray.append( traitinfo )
#calculate correlation with slow method
else:
correlationArray = self.calCorrelation(sourceTrait, self.readDB(StrainIds, prefix2, dbId2) )
correlationArray.sort(self.cmpCorr) #XZ: Do not forget the sort step
if not self.returnNumber:
correlationArray = correlationArray[:100]
else:
if self.returnNumber < len(correlationArray):
correlationArray = correlationArray[:self.returnNumber]
NN = len(correlationArray)
for i in range(NN):
nOverlap = correlationArray[i][-1]
corr = correlationArray[i][-2]
if nOverlap < 3:
corrPValue = 1.0
else:
if abs(corr) >= 1.0:
corrPValue = 0.0
else:
ZValue = 0.5*log((1.0+corr)/(1.0-corr))
ZValue = ZValue*sqrt(nOverlap-3)
corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
correlationArray[i].append(corrPValue)
if self.sort == 'pvalue':
correlationArray.sort(self.cmpPValue)
if prefix2 == 'Publish':
self.contents.append("RecordID\tCorrelation\t#Strains\tp-value")
elif prefix2 == 'Geno':
self.contents.append("Locus\tCorrelation\t#Strains\tp-value")
else:
pass
if prefix2 == 'Publish' or prefix2 == 'Geno':
for item in correlationArray:
self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item))
else:
id = self.data.getvalue('id')
if id == 'yes':
self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value\tGeneID")
for item in correlationArray:
query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0])
self.cursor.execute(query)
results = self.cursor.fetchall()
if not results:
item = item + [None]
else:
item = item + list(results[0])
self.contents.append("%s\t%2.6f\t%d\t%2.6f\t%s" % tuple(item))
elif id == 'only':
self.contents.append("GenID")
for item in correlationArray:
query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0])
self.cursor.execute(query)
results = self.cursor.fetchall()
if not results:
self.contents.append('None')
else:
self.contents.append(results[0][0])
else:
self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value")
for item in correlationArray:
self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item))