aboutsummaryrefslogtreecommitdiff
path: root/web/webqtl/management/GenoUpdate.py
diff options
context:
space:
mode:
Diffstat (limited to 'web/webqtl/management/GenoUpdate.py')
-rwxr-xr-xweb/webqtl/management/GenoUpdate.py1279
1 files changed, 1279 insertions, 0 deletions
diff --git a/web/webqtl/management/GenoUpdate.py b/web/webqtl/management/GenoUpdate.py
new file mode 100755
index 00000000..6ee87dec
--- /dev/null
+++ b/web/webqtl/management/GenoUpdate.py
@@ -0,0 +1,1279 @@
+"""
+Maintainnce module. Update Genotype data, user can update the Marker
+one by one through web interface, or batch update one Population
+through submit genotype file
+"""
+
+import string
+import os
+
+from htmlgen import HTMLgen2 as HT
+
+from base.templatePage import templatePage
+from base import webqtlConfig
+from utility import webqtlUtil
+from dbFunction import webqtlDatabaseFunction
+
+
+
+"""
+The Fields of Geno, GenoXRef table that be shown to user for updating
+"""
+MarkerSpeciesInfoField = ['Name', 'Chr', 'Mb', 'Sequence', 'Source']
+MarkerGroupInfoField = ['cM', 'Used_for_mapping']
+MarkerInfoField = MarkerSpeciesInfoField + MarkerGroupInfoField
+markerName_Feild_Separator = '_and_'
+
+
+# retrieve all of the Inbred Set names and group them by Species
+def retrieveSpeciesInbredSetGroup(cursor):
+ """
+ @type cursor: MySQLdb.connect.cursor
+ rtype: dictionary
+ return: dictionary, the key are the name of Species, the value are
+ the InbredSet Names that related with the Species
+ """
+
+ SpeciesInbredSet={}
+ cursor.execute("""
+ SELECT
+ Species.Id, Species.Name
+ FROM
+ Species, InbredSet
+ WHERE
+ Species.Id=InbredSet.SpeciesId AND
+ MappingMethodId = 1
+ GROUP BY
+ Species.Id
+ """)
+ species=cursor.fetchall()
+
+ for item in species:
+ SpeciesId, SpeciesName = item
+ cursor.execute("SELECT distinct(InbredSet.Name) FROM InbredSet, GenoFreeze, GenoXRef WHERE SpeciesId=%d and GenoFreeze.InbredSetId = InbredSet.Id and GenoXRef.GenoFreezeId = GenoFreeze.Id and GenoXRef.Used_for_mapping='Y' " % SpeciesId)
+ InbredSetNames=cursor.fetchall()
+
+ InbredSetNameList=[]
+ for InbredSetName in InbredSetNames:
+ if InbredSetName[0]=='BXD300':
+ continue
+ InbredSetNameList.append(InbredSetName[0])
+ SpeciesInbredSet[SpeciesName]=InbredSetNameList
+
+ return SpeciesInbredSet
+
+
+#XZ: This function will be called in many places.
+# Each caller might organize the result in different way.
+# So the raw database results are returned.
+def retrieveGenoCode(cursor, InbredSetName):
+
+ cursor.execute("""
+ SELECT
+ AlleleType, AlleleSymbol, DatabaseValue
+ FROM
+ GenoCode, InbredSet
+ WHERE
+ InbredSet.Name = '%s' AND
+ InbredSetId = InbredSet.Id
+ """ % InbredSetName )
+ results = cursor.fetchall()
+
+ GenoCode = []
+
+ for one_result in results:
+ GenoCode.append(one_result)
+
+ return GenoCode
+
+
+def retrieveGeneticTypeOfInbredSet(cursor, InbredSetName):
+
+ GeneticType = ''
+
+ cursor.execute("""
+ SELECT
+ GeneticType
+ FROM
+ InbredSet
+ WHERE
+ InbredSet.Name=%s
+ """, InbredSetName)
+ result=cursor.fetchone()
+
+ if result:
+ GeneticType = result[0]
+
+ return GeneticType
+
+
+
+
+#XZ: For one group, retrieve the list of all strains that are in StrainXRef and used for mapping
+def retrieveStrainUsedForMapping(cursor, GroupName):
+ """
+ @type cursor: MySQLdb.connect.cursor
+ @type GroupName: string
+ @param GroupName: In MySQL table, it's called Inbred Set name, in GeneNetwork's Homepage, it's called group
+
+ @rtype: list
+ @return: The Strain's names that related with the Inbred Set
+ """
+
+ cursor.execute("""
+ SELECT
+ Strain.Name
+ FROM
+ Strain, StrainXRef, InbredSet
+ WHERE
+ InbredSet.Name = '%s' AND
+ StrainXRef.InbredSetId=InbredSet.Id AND
+ StrainXRef.StrainId = Strain.Id AND
+ StrainXRef.Used_for_mapping = 'Y'
+ ORDER BY
+ StrainXRef.OrderId
+ """ % GroupName)
+ results = cursor.fetchall()
+
+ StrainList=[]
+ for item in results:
+ StrainList.append(item[0])
+
+ return StrainList
+
+
+#XZ: For one group, retrieve the dictionary of all strain id, name pairs that are in StrainXRef and used for mapping
+def retrieveStrainNameIdUsedForMapping(cursor, GroupName):
+ """
+ @type cursor: MySQLdb.connect.cursor
+ @type GroupName: string
+ @param GroupName: In MySQL table, it's called Inbred Set name, in GeneNetwork's Homepage, it's called group
+
+ @rtype: dictionary
+ @return: dictionary, the key is Strain's name, the value is Strain's Id
+ """
+
+ StrainNameId = {}
+
+ cursor.execute("""
+ SELECT
+ Strain.Name, Strain.Id
+ FROM
+ Strain, StrainXRef, InbredSet
+ WHERE
+ InbredSet.Name = '%s' AND
+ StrainXRef.InbredSetId=InbredSet.Id AND
+ StrainXRef.StrainId = Strain.Id AND
+ StrainXRef.Used_for_mapping = 'Y'
+ ORDER BY
+ StrainXRef.OrderId
+ """ % GroupName)
+ results = cursor.fetchall()
+
+ for item in results:
+ StrainNameId[item[0]] = item[1]
+
+ return StrainNameId
+
+
+
+# retrieve the strain's id by name, the Strain should bind with Inbred Set
+#if the strain's name cann't be found, the id will be set to 'None'
+def retrieveStrainIds(cursor, StrainList, InbredSetName):
+ """
+ @type cursor: MySQLdb.connect.cursor
+ @type StrainList: list
+ @param StrainList: the list of Strains' Name
+ @type InbredSetName: string
+
+ @rtype: dictionary
+ @return: dictionary, the key is Strain's name, the value is Strain's Id
+ """
+
+ StrainIds={}
+ for Strain in StrainList:
+ cursor.execute("""
+ SELECT
+ Strain.Id
+ FROM
+ Strain,StrainXRef,InbredSet
+ WHERE
+ Strain.Id=StrainXRef.StrainId AND
+ StrainXRef.InbredSetId=InbredSet.Id AND
+ Strain.Name=%s AND
+ InbredSet.Name=%s
+ """, (Strain, InbredSetName))
+ result=cursor.fetchone()
+ if result:
+ StrainIds[Strain]=result[0]
+ else:
+ StrainIds[Strain]=None
+
+ return StrainIds
+
+
+
+# retrieve the GenoFreezeId
+def retrieveGenoFreezeId(cursor, InbredSetName):
+ """
+ @type cursor: MySQLdb.connect.cursor
+ @type InbredSetName: string
+
+ @rtype: int
+ @return: the GenoFreezeId related with the Inbred Set's name
+ """
+
+ cursor.execute("""
+ SELECT
+ GenoFreeze.Id
+ FROM
+ InbredSet, GenoFreeze
+ WHERE
+ GenoFreeze.InbredSetId=InbredSet.Id AND
+ InbredSet.Name=%s
+ """, InbredSetName)
+ result=cursor.fetchone()
+
+ if result:
+ return result[0]
+ else:
+ return None
+
+
+# retrieve the DataId
+def retrieveDataId(cursor, GenoId, InbredSetName):
+ """
+ @type cursor: MySQLdb.connect.cursor
+ @type GenoId: int
+ @type InbredSetName: int
+
+ @rtype: int
+ @return: the DataId relate with the Geno(Marker) and the Inbred Set
+ """
+
+ cursor.execute("""
+ SELECT
+ GenoXRef.DataId
+ FROM
+ GenoXRef, GenoFreeze, InbredSet
+ WHERE
+ GenoXRef.GenoFreezeId=GenoFreeze.Id AND
+ GenoFreeze.InbredSetId=InbredSet.Id AND
+ GenoXRef.GenoId=%s AND
+ InbredSet.Name=%s
+ """, (GenoId, InbredSetName))
+ result=cursor.fetchone()
+
+ if result:
+ return result[0]
+ else:
+ return None
+
+
+# retrieve the max Id from GenoData table
+def retrieveMaxGenoDataId(cursor):
+ """
+ @type cursor: MySQLdb.connect.cursor
+
+ @rtype: int
+ @return: the maximal Id of the Data table
+ """
+
+ cursor.execute('SELECT max(Id) FROM GenoData')
+ results = cursor.fetchone()
+
+ return results[0]
+
+
+# retrieve the max Id from Geno table
+def retrieveMaxGenoId(cursor):
+ """
+ @type cursor: MySQLdb.connect.cursor
+
+ @rtype: int
+ @return: the maximal Id of the Geno table
+ """
+
+ cursor.execute('SELECT max(Id) FROM Geno')
+ results = cursor.fetchone()
+
+ return results[0]
+
+
+# retrieve the strain names related with a data.Id
+# Note that for one group, even if one strain is labelled as Used_for_mapping in StrainXRef table,
+# if the allele value for this strain is unknown, there is no record for this strain along with this group in GenoData table.
+# So the list of strains returned by this function <= list of strains returned by function retrieveStrainUsedForMapping.
+def retrieveDataStrains(cursor, DataId):
+ """
+ @type cursor: MySQLdb.connect.cursor
+ @type DataId: int
+
+ @rtype: list
+ @return: the names list of the Strains that related with the DataId
+ """
+
+ cursor.execute("SELECT Strain.Name FROM Strain, GenoData WHERE GenoData.StrainId=Strain.Id AND GenoData.Id=%s", DataId)
+ results=cursor.fetchall()
+
+ Strains=[]
+ for item in results:
+ Strains.append(item[0])
+
+ return Strains
+
+
+
+def retrieveMarkerNameForGroupByRange(cursor, InbredSetName, Chr, MbStart, MbEnd):
+
+ MarkerName = []
+
+ SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName)
+
+ GenoFreezeId = retrieveGenoFreezeId(cursor, InbredSetName)
+
+ MbStartClause = ''
+ MbEndClause = ''
+
+ try:
+ MbStartClause = 'and Mb >= %s ' % float(MbStart)
+ except:
+ pass
+
+ try:
+ MbEndClause = 'and Mb <= %s' % float(MbEnd)
+ except:
+ pass
+
+
+ cmd = "SELECT Geno.Name FROM Geno, GenoXRef WHERE Geno.SpeciesId=%s and Chr='%s' " % (SpeciesId, Chr) + MbStartClause + MbEndClause + " and GenoXRef.GenoFreezeId=%s and GenoXRef.GenoId=Geno.Id and GenoXRef.Used_for_mapping='Y' order by Mb" % (GenoFreezeId)
+
+ cursor.execute(cmd)
+
+ results = cursor.fetchall()
+ for one_result in results:
+ MarkerName.append( one_result[0] )
+
+ return MarkerName
+
+
+
+# retrive the Marker's infomation from Geno and GenoXRef table,
+# the information includes the Id of the marker matchs and all of the MarkerInfoField that defined upper
+def retrieveMarkerInfoForGroup(cursor, MarkerName, InbredSetName):
+ """
+ @type cursor: MySQLdb.connect.cursor
+ @type MarkerName: string
+
+ @rtype: list
+ @return: the Marker's Id, Name, Chr, cM, Mb, Sequence, Source
+ """
+
+
+ SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName)
+
+ GenoFreezeId = retrieveGenoFreezeId(cursor, InbredSetName)
+
+ cmd = ','.join( MarkerInfoField )
+ cmd = "SELECT Geno.Id," + cmd + " FROM Geno, GenoXRef WHERE Geno.SpeciesId=%s and Geno.Name='%s' and GenoXRef.GenoFreezeId=%s and GenoXRef.GenoId=Geno.Id" % (SpeciesId, MarkerName, GenoFreezeId)
+ cursor.execute(cmd)
+ result = cursor.fetchone()
+
+ if result:
+ return result
+ else:
+ return None
+
+
+def retrieveMarkerPositionForSpecies(cursor, GenoId):
+
+ Chr = ''
+ Mb = ''
+
+ cursor.execute( "select Chr, Mb from Geno where Id=%s" % GenoId )
+ result = cursor.fetchone()
+
+ Chr = result[0]
+ Mb = result[1]
+
+ return Chr, Mb
+
+
+def checkIfMarkerInSpecies (cursor, MarkerName, InbredSetName):
+
+ cmd = "SELECT Geno.Id FROM Geno, InbredSet, Species WHERE Geno.SpeciesId=Species.Id AND Geno.Name='%s' and InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (MarkerName, InbredSetName)
+ cursor.execute(cmd)
+ result = cursor.fetchone()
+
+ if result:
+ return result
+ else:
+ return None
+
+
+
+
+# retrive the Marker's Used_for_mapping status from MySQL
+# for one marker, if we want it be contains in the special genotype file, we can set its value in Used_for_mapping column to 'Y' in the GenoXRef table.
+# In GenoXRef table, the default value of column Used_for_mapping is 'N'.
+# GenoXRef table is the relationship of the Marker and the allele value that this marker in special genotype
+def mappingForThisGroup(cursor, GenoFreezeId, GenoId):
+ """
+ @type cursor: MySQLdb.connect.cursor
+ @type MarkerName: string
+ @type InbredSetName: string
+
+ @rtype: boolean
+ @return: the status that if the marker's exprssion value in special Inbred Set will be hide(not shown in genotype file)
+ """
+
+ cursor.execute("""
+ SELECT
+ Used_for_mapping
+ FROM
+ GenoXRef
+ WHERE
+ GenoFreezeId = %s AND
+ GenoId = %s
+ """, (GenoFreezeId, GenoId))
+ result = cursor.fetchone()
+
+ Used_for_mapping = False
+ if result:
+ if result[0] == 'Y':
+ Used_for_mapping = True
+
+ return Used_for_mapping
+
+
+# Retrieve the allele values of a Marker in specific genotype
+#
+# 1. Retrieve strain name and allele value from GenoData table
+# 2. Put the result into dictionary, the key is strain name. The value is allele (-1, 0, 1).
+#
+# Note even one strain is used for mapping for one group in GenoXRef table. When its genotype is unknown,
+# it has no record in GenoData table (e.g., BXD102 strain for marker rs6376963).
+# In this case, the dictionary key doesn't include this strain.
+def retrieveAllele (cursor, GenoFreezeId, GenoId):
+ """
+ @type cursor: MySQLdb.connect.cursor
+ @type MarkerName: string
+ @type InbredSetName: string
+
+ @rtype: dictionary
+ @return: dictionary, the keys are strain names, the values are alleles
+ that the Marker in specials Inbred Set
+ """
+
+ Alleles = {}
+
+ #retrieve the strains' name and their allele values
+ cursor.execute("""
+ SELECT
+ Strain.Name, GenoData.Value
+ FROM
+ Strain, GenoData, GenoXRef
+ WHERE
+ GenoXRef.GenoFreezeId=%s AND
+ GenoXRef.GenoId=%s AND
+ GenoXRef.DataId=GenoData.Id AND
+ GenoData.StrainId=Strain.Id
+ """, (GenoFreezeId, GenoId))
+ results = cursor.fetchall()
+
+ # set the allele value of the strain that appears in Data to the value from Data
+ for item in results:
+ Alleles[item[0]]=item[1]
+
+ return Alleles
+
+
+
+def retrieveGroupNeedExported (cursor, GenoId):
+
+ Groups = []
+
+ cursor.execute("""
+ SELECT
+ InbredSet.Name
+ FROM
+ InbredSet, GenoFreeze, GenoXRef
+ WHERE
+ Used_for_mapping = 'Y' AND
+ GenoXRef.GenoId = %s AND
+ GenoXRef.GenoFreezeId = GenoFreeze.Id AND
+ GenoFreeze.InbredSetId = InbredSet.Id
+ """, (GenoId) )
+ results = cursor.fetchall()
+
+ if results:
+ for one_result in results:
+ Groups.append( one_result[0] )
+
+ return Groups
+
+
+def get_chr_num (cursor, Chr='', SpeciesId=0):
+
+ chr_num = 99
+
+ cmd = "SELECT OrderId FROM Chr_Length WHERE Name='%s' and SpeciesId=%s " % (Chr, SpeciesId)
+
+ cursor.execute(cmd)
+ result = cursor.fetchone()
+
+ if result:
+ chr_num = result[0]
+
+ return chr_num
+
+
+
+def addGeno(cursor, GenoId, InbredSetName, MarkerWebID, fd):
+
+ SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName)
+
+ Name = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Name' )
+ Chr = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Chr' )
+ Mb = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Mb' )
+ Sequence = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Sequence' )
+ Source = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Source' )
+
+ chr_num = get_chr_num (cursor, Chr, SpeciesId)
+
+ cmd = "INSERT INTO Geno (Id, SpeciesId, Name, Marker_Name, Chr, Mb, Sequence, Source, chr_num) VALUES (%s, %s, '%s', '%s', '%s', %s, '%s', '%s', %s )" % (GenoId, SpeciesId, Name, Name, Chr, Mb, Sequence, Source, chr_num)
+ cursor.execute(cmd)
+
+
+
+def updateGeno(cursor, GenoId, InbredSetName, MarkerWebID, fd):
+
+ SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName)
+
+ Chr = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Chr' )
+ cmd = "UPDATE Geno SET Chr='%s' WHERE Id=%s" % (Chr, GenoId)
+ cursor.execute(cmd)
+
+ chr_num = get_chr_num (cursor, Chr, SpeciesId)
+ cmd = "UPDATE Geno SET chr_num=%s WHERE Id=%s" % (chr_num, GenoId)
+ cursor.execute(cmd)
+
+ Mb = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Mb' )
+ cmd = "UPDATE Geno SET Mb=%s WHERE Id=%s" % (Mb, GenoId)
+ cursor.execute(cmd)
+
+ Sequence = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Sequence' )
+ cmd = "UPDATE Geno SET Sequence='%s' WHERE Id=%s" % (Sequence, GenoId)
+ cursor.execute(cmd)
+
+ Source = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Source' )
+ cmd = "UPDATE Geno SET Source='%s' WHERE Id=%s" % (Source, GenoId)
+ cursor.execute(cmd)
+
+
+def updateGenoXRef(cursor, GenoFreezeId, GenoId, MarkerWebID, fd):
+
+ cM = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'cM' )
+ cmd = "UPDATE GenoXRef SET cM=%s WHERE GenoFreezeId=%s AND GenoId=%s" % (cM, GenoFreezeId, GenoId)
+ cursor.execute(cmd)
+
+ Used_for_mapping = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Used_for_mapping')
+
+ if Used_for_mapping == 'on':
+ cmd = "UPDATE GenoXRef SET Used_for_mapping='Y' WHERE GenoFreezeId=%s AND GenoId=%s" % (GenoFreezeId, GenoId)
+ else:
+ cmd = "UPDATE GenoXRef SET Used_for_mapping='N' WHERE GenoFreezeId=%s AND GenoId=%s" % (GenoFreezeId, GenoId)
+ cursor.execute(cmd)
+
+
+
+def addGenoXRef(cursor, GenoFreezeId, GenoId, DataId, MarkerWebID, fd):
+
+ cM = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'cM')
+
+ Used_for_mapping = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Used_for_mapping')
+
+ Used_for_mapping_db_value = 'N'
+ if Used_for_mapping == 'on':
+ Used_for_mapping_db_value = 'Y'
+
+ cmd = "INSERT INTO GenoXRef (GenoFreezeId, GenoId, DataId, cM, Used_for_mapping) VALUES (%s, %s, %s, %s, '%s')" % (GenoFreezeId, GenoId, DataId, cM, Used_for_mapping_db_value)
+
+ cursor.execute(cmd)
+
+
+
+def insertGenoData(cursor, InbredSetName, DataId, MarkerWebID, fd):
+
+ StrainList = retrieveStrainUsedForMapping (cursor, InbredSetName)
+ StrainIds = retrieveStrainIds(cursor, StrainList, InbredSetName)
+
+ for Strain in StrainList:
+ if fd.formdata.has_key( MarkerWebID + markerName_Feild_Separator + Strain ):
+ value = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + Strain )
+
+ # XZ: The legitimate values are hard coded. Should be dynamical (from database).
+ try:
+ int_value = int(float(value))
+
+ if int_value in (0, 1, -1):
+ cmd = "INSERT INTO GenoData VALUES(%d,%d,%s)"%(DataId, StrainIds[Strain], int_value)
+ cursor.execute(cmd)
+ except:
+ pass
+
+
+#XZ: This function is to compare the input position (Chr, Mb) with position in database.
+# It should be executed before update database record.
+def getAllGroupsNeedExported(cursor, GroupNeedExport=[], GenoId=0, Chr='', Mb=''):
+
+ db_Chr, db_Mb = retrieveMarkerPositionForSpecies(cursor, GenoId)
+
+ if str(Chr) == str(db_Chr) and str(Mb) == str(db_Mb):
+ pass
+ else:
+ temp = retrieveGroupNeedExported (cursor, GenoId)
+ for one_group in temp:
+ try:
+ GroupNeedExport.index(one_group)
+ except:
+ GroupNeedExport.append(one_group)
+
+ return GroupNeedExport
+
+
+
+
+class GenoUpdate(templatePage):
+
+ def __init__(self, fd):
+
+ templatePage.__init__(self, fd)
+
+ # get mysql connection, if not, show error
+ if not self.openMysql():
+ heading = "Geno Updating"
+ detail = ["Can't connect to MySQL server"]
+ self.error(heading=heading,detail=detail)
+ return
+
+
+ self.dict['title'] = 'Geno Updating'
+
+ # status is the switch, direct what's the next step
+ try:
+ status = fd.formdata.getvalue('status')
+ except:
+ status = ''
+
+ if fd.formdata.getvalue('submit')=='Clear':
+ status=''
+
+ if not status: # show
+ self.dict['body']=self.showSelectionPage()
+ elif status=='search' or status == 'addNewMarker':
+ InbredSetName = fd.formdata.getvalue('InbredSetName')
+ Chr = fd.formdata.getvalue('Chr')
+
+ if not InbredSetName:
+ self.dict['body']= "Please select the population."
+ return
+ elif not Chr:
+ self.dict['body']= "Please input Chr."
+ return
+ else:
+ self.dict['body']=self.showAllMarkers (InbredSetName, Chr, fd)
+
+ elif status == 'editMarkerTable':
+ self.dict['body'] = self.editMarkerTable(fd)
+
+ elif status == 'checkMarkerHasBeenInGroup': # check if there is anything changed.
+ InbredSetName = fd.formdata.getvalue('InbredSetName')
+ Marker = fd.formdata.getvalue('Name')
+ self.dict['body'] = self.checkMarkerHasBeenInGroup (InbredSetName, Marker, fd)
+
+ elif status=='changeMarker': #insert new marker
+ InbredSetName = fd.formdata.getvalue('InbredSetName')
+ self.dict['body']=self.changeMarker(InbredSetName, fd)
+
+ else: #this part is used to test, the proceduce won't come here in normal cycle
+ HTTable = HT.TableLite(border=0, cellspacing=1, cellpadding=1,align="center")
+ for key in fd.formdata.keys():
+ HTTable.append(HT.TR(HT.TD(key), HT.TD(':'), HT.TD(fd.formdata.getvalue(key))))
+ self.dict['body'] = HTTable
+
+
+
+
+ # this is the first page, user upload their genotype file here, or input
+ # which marker they want to update
+ def showSelectionPage(self):
+ """
+ The first page, in this page, user can upload a genotype file for batch updating,
+ or enter a Marker for one by one updating
+
+ @rtype: string
+ @return: HTML
+ """
+
+ # get the InbredSet Name list
+ SpeciesInbredSet = retrieveSpeciesInbredSetGroup(self.cursor)
+
+ # generate homepage
+
+ HTTableLite_Population = HT.TableLite(border=0, width="100%")
+
+ HTTD_InbredSet = HT.TD(width="30%")
+
+ HTSelect_InbredSetNames = HT.Select(name='InbredSetName')
+ HTSelect_InbredSetNames.append("")
+ for SpeciesName in SpeciesInbredSet.keys():
+ HT_OptGroup_Species=HT.Optgroup()
+ HT_OptGroup_Species.label=SpeciesName
+ for InbredSetName in SpeciesInbredSet[SpeciesName]:
+ HT_OptGroup_Species.append(InbredSetName)
+ HTSelect_InbredSetNames.append(HT_OptGroup_Species)
+
+ HTTD_InbredSet.append( HT.Font(HT.Strong('Group (required) '), color="red") )
+ HTTD_InbredSet.append(HTSelect_InbredSetNames)
+
+ HTTableLite_Population.append(HT.TR(HTTD_InbredSet))
+
+ HTTableLite_Marker = HT.TableLite(border=0, width="100%")
+ HTTD_Chr = HT.TD()
+ HTTD_Chr.append( HT.Font(HT.Strong('Chr (required) '), color="red") )
+ HTTD_Chr.append(HT.Input(name='Chr', size=3))
+ HTTD_Mb = HT.TD()
+ HTTD_Mb.append(HT.Font(HT.Strong('Mb')), ' from ')
+ HTTD_Mb.append(HT.Input(name='MbStart', size=10))
+ HTTD_Mb.append(' to ')
+ HTTD_Mb.append(HT.Input(name='MbEnd', size=10))
+ HTTableLite_Marker.append(HT.TR(HTTD_Chr), HT.TR(), HT.TR(HTTD_Mb) )
+
+
+
+ HTTableLite_Search = HT.TableLite(border=1, width="100%")
+ HTTableLite_Search.append(
+ HT.TR(HT.TD(HTTableLite_Population, height="100")),
+ HT.TR(HT.TD("Enter Chr and Mb range", HT.BR(), HT.BR(),
+ HTTableLite_Marker,
+ height="100"))
+ )
+
+
+ HTInput_Submit = HT.Input(type='submit', name='submit', value='Submit',Class="button")
+ HTInput_Clear = HT.Input(type='submit', name='submit', value='Clear', Class="button")
+ HTInput_FormId = HT.Input(type='hidden', name='FormID', value='updGeno')
+ HTInput_Status = HT.Input(type='hidden', name='status', value='search')
+
+ HTForm_Search = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, 'main.py'), \
+ enctype= 'multipart/form-data', submit='')
+ HTForm_Search.append(HTTableLite_Search)
+ HTForm_Search.append(HTInput_Submit)
+ HTForm_Search.append(HTInput_Clear)
+
+ HTForm_Search.append(HTInput_FormId)
+ HTForm_Search.append(HTInput_Status)
+
+ HTTableLite_Content = HT.TableLite(border=1, width="100%")
+ HTTableLite_Content.append(HT.TR(HT.TD(HTForm_Search, width="50%"), \
+ HT.TD(HT.Font(HT.Strong("Instructions:"), HT.BR(),HT.BR(), "The \"from\" and \"to\" inputs for Mb range are optional.", HT.BR(),HT.BR(), "If only the \"from\" input is provided, the result will be all markers from the input position to the end of chromosome.", HT.BR(),HT.BR(), "If only the \"to\" input is provided, the result will be all markers from the beginning of the chromosome to the input position.", HT.BR(),HT.BR(), "If no input is provided for Mb range, the result will be all markers on the chromosome."), valign='top', width="50%") \
+ ))
+
+ return HTTableLite_Content
+
+
+
+
+ def searchMappingMarkerInDB (self, InbredSetName="", Chr='', MbStart='', MbEnd=''):
+ """
+ Show Marker's information for updating or inserting
+
+ @type InbredSetName: string
+ @type MarkerName: string
+
+ @rtype: string
+ @return: The HTML form that contains the Marker's information
+ """
+
+
+ MarkerInfoDic = {}
+
+ MarkerNamesByRange = retrieveMarkerNameForGroupByRange(self.cursor, InbredSetName, Chr, MbStart, MbEnd)
+
+ for one_MarkerName in MarkerNamesByRange:
+ one_MarkerGroupInfo = retrieveMarkerInfoForGroup (self.cursor, one_MarkerName, InbredSetName)
+ MarkerInfoDic[ one_MarkerName ] = one_MarkerGroupInfo
+
+ return MarkerNamesByRange, MarkerInfoDic
+
+
+
+ def showAllMarkers( self, InbredSetName, Chr, fd ):
+
+ MbStart = fd.formdata.getvalue('MbStart')
+ MbEnd = fd.formdata.getvalue('MbEnd')
+
+ inputStatus = fd.formdata.getvalue('status')
+
+ newMarkerNameQuantityDic = {}
+ MarkerNameAdded = []
+
+ MarkerNames, MarkerInfoDic = self.searchMappingMarkerInDB (InbredSetName=InbredSetName, Chr=Chr, MbStart=MbStart, MbEnd=MbEnd)
+
+ MainTable = HT.TableLite(border=1, cellspacing=1, cellpadding=1,align="left")
+
+ if inputStatus == 'search':
+
+
+ InputTable = HT.TableLite(border=1, cellspacing=1, cellpadding=1,align="left")
+
+ InputTable.append( HT.TR( HT.TD( HT.Textarea(name="InputNewMarker", rows=10, cols=20)),
+ HT.TD(HT.Font( "Add one input per line.", HT.BR(), HT.BR(), \
+ "Each input must be in the format of: existing marker name,quantity", HT.BR(), HT.BR(), \
+ "For instance, the input rs6376963, 2 will add two markers after rs6376963", HT.BR(), HT.BR(), \
+ "The input existing marker name must have been shown in the table below.", HT.BR(), HT.BR(), color="red"), \
+ HT.Input(type='submit', name='inputmarker_submit', value='Add new markers', Class="button", onClick= "changeStatusSubmit(this.form, 'addNewMarker');" ) ) ) )
+
+ MainTable.append( HT.TR(HT.TD(InputTable)) )
+ else:
+ InputNewMarkerString = fd.formdata.getvalue('InputNewMarker')
+
+ InputNewMarkerLines = InputNewMarkerString.split('\n')
+ for one_line in InputNewMarkerLines:
+ one_line = one_line.strip()
+ if len(one_line) > 0:
+ one_line_tokens = one_line.split(',')
+ try:
+ first_token = one_line_tokens[0].strip()
+ second_token = one_line_tokens[1].strip()
+ second_token = int( second_token )
+ if first_token in MarkerNames:
+ newMarkerNameQuantityDic[ first_token ] = second_token
+ except:
+ pass
+
+
+ MarkerTable = HT.TableLite(border=1, cellspacing=1, cellpadding=1,align="left")
+
+ HeaderRow = HT.TR()
+
+
+ for one_field in MarkerSpeciesInfoField:
+ HeaderRow.append( HT.TD(one_field) )
+
+ for one_field in MarkerGroupInfoField:
+ HeaderRow.append( HT.TD(one_field) )
+
+ GenoFreezeId = retrieveGenoFreezeId(self.cursor, InbredSetName)
+ StrainList = retrieveStrainUsedForMapping (self.cursor, InbredSetName)
+
+ for one_strain in StrainList:
+ HeaderRow.append( HT.TD(one_strain) )
+
+ MarkerTable.append( HeaderRow )
+
+
+ for one_MarkerName in MarkerNames:
+ one_MarkerGroupInfo = MarkerInfoDic[ one_MarkerName ]
+ oneMarkerRow = self.showOneMarker (InbredSetName=InbredSetName, MarkerName=one_MarkerName, suffix="", MarkerGroupInfo=one_MarkerGroupInfo, StrainList=StrainList, marker_type='existed')
+ MarkerTable.append( oneMarkerRow )
+
+ if newMarkerNameQuantityDic.has_key(one_MarkerName):
+ for i in range(0, newMarkerNameQuantityDic[one_MarkerName]):
+ MarkerNameAdded.append( one_MarkerName + '_add_' + str(i) )
+ oneMarkerRow = self.showOneMarker (InbredSetName=InbredSetName, MarkerName=one_MarkerName, suffix='_add_' + str(i), MarkerGroupInfo=one_MarkerGroupInfo, StrainList=StrainList, marker_type='add')
+ MarkerTable.append( oneMarkerRow )
+
+
+
+ MarkerTable.append( HT.TR(HT.TD( HT.Input(type='submit', name='markertable_submit', value='Edit marker table',Class="button", onClick= "changeStatusSubmit(this.form, 'editMarkerTable');") )) )
+
+ MainTable.append( HT.TR(HT.TD(MarkerTable)) )
+
+
+ HTInput_Submit = HT.Input(type='hidden', name='submit', value='Submit',Class="button")
+ HTInput_FormId = HT.Input(type='hidden', name='FormID', value='updGeno')
+ HTInput_Status = HT.Input(type='hidden', name='status', value='')
+ HTInput_InbredSetName = HT.Input(type='hidden', name='InbredSetName', value=InbredSetName)
+ HTInput_Chr = HT.Input(type='hidden', name='Chr', value=Chr)
+ HTInput_MbStart = HT.Input(type='hidden', name='MbStart', value=MbStart)
+ HTInput_MbEnd = HT.Input(type='hidden', name='MbEnd', value=MbEnd)
+ HTInput_MarkerNamesExisted = HT.Input(type='hidden', name='MarkerNamesExisted', value=','.join(MarkerNames) )
+ HTInput_MarkerNamesAdded = HT.Input(type='hidden', name='MarkerNamesAdded', value=','.join(MarkerNameAdded) )
+
+
+ HTForm_showAllMarkers = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, 'main.py'), enctype= 'multipart/form-data', submit=HTInput_Submit)
+
+ HTForm_showAllMarkers.append( MainTable )
+ HTForm_showAllMarkers.append(HTInput_FormId)
+ HTForm_showAllMarkers.append(HTInput_Status)
+ HTForm_showAllMarkers.append(HTInput_InbredSetName)
+ HTForm_showAllMarkers.append(HTInput_Chr)
+ HTForm_showAllMarkers.append(HTInput_MbStart)
+ HTForm_showAllMarkers.append(HTInput_MbEnd)
+ HTForm_showAllMarkers.append(HTInput_MarkerNamesExisted)
+ HTForm_showAllMarkers.append(HTInput_MarkerNamesAdded)
+
+ return HTForm_showAllMarkers
+
+
+
+ def showOneMarker (self, InbredSetName="", MarkerName="", suffix="", MarkerGroupInfo=[], StrainList=[], marker_type=''):
+
+ GenoInfo={}
+
+ #XZ: The first item of MarkerInfo is Geno.Id
+ GenoId = MarkerGroupInfo[0]
+
+ for i in range(1, len(MarkerGroupInfo)):
+ if MarkerGroupInfo[i] != None:
+ GenoInfo[ MarkerInfoField[i-1] ] = str(MarkerGroupInfo[i])
+ else:
+ GenoInfo[ MarkerInfoField[i-1] ] = ''
+
+ if GenoInfo['Used_for_mapping'] == 'Y':
+ GenoInfo['Used_for_mapping'] = True
+ else:
+ GenoInfo['Used_for_mapping'] = False
+
+
+ MarkerRow = HT.TR()
+
+ # Species level info
+ for i in range(0, len(MarkerSpeciesInfoField)):
+ if MarkerSpeciesInfoField[i] == 'Name':
+ if marker_type == 'existed':
+ MarkerRow.append( HT.TD(GenoInfo['Name']) )
+ else:
+ MarkerRow.append(HT.TD(HT.Input(name = MarkerName + suffix + markerName_Feild_Separator + MarkerSpeciesInfoField[i], size=20, maxlength=500, value=MarkerName + suffix )))
+ else:
+ MarkerRow.append(HT.TD(HT.Input(name = MarkerName + suffix + markerName_Feild_Separator + MarkerSpeciesInfoField[i], size=10, maxlength=500, value=GenoInfo[MarkerSpeciesInfoField[i]])))
+
+ # Group level info
+ for i in range(0, len(MarkerGroupInfoField)):
+ if MarkerGroupInfoField[i] != 'Used_for_mapping':
+ MarkerRow.append( HT.TD(HT.Input(name = MarkerName + suffix + markerName_Feild_Separator + MarkerGroupInfoField[i], size=10, value=GenoInfo[MarkerGroupInfoField[i]])))
+ else:
+ MarkerRow.append( HT.TD(HT.Input(type='checkbox', name= MarkerName + suffix + markerName_Feild_Separator + 'Used_for_mapping', checked=GenoInfo['Used_for_mapping'] )))
+
+ # retrive Marker allele values
+ GenoFreezeId = retrieveGenoFreezeId(self.cursor, InbredSetName)
+ Alleles = retrieveAllele (self.cursor, GenoFreezeId, GenoId)
+
+ for i in range(0, len(StrainList)):
+ try:
+ Value = Alleles[StrainList[i]]
+ except:
+ Value = 'X' # 'X' is the symbol for unknown allele
+ MarkerRow.append( HT.TD(HT.Input(name = MarkerName + suffix + markerName_Feild_Separator + StrainList[i], size=3, maxlength=5, value=Value)))
+
+
+ return MarkerRow
+
+
+ def editMarkerTable (self, fd):
+
+ InbredSetName = fd.formdata.getvalue('InbredSetName')
+ Chr = fd.formdata.getvalue('Chr')
+
+ MbStart = fd.formdata.getvalue('MbStart')
+ MbEnd = fd.formdata.getvalue('MbEnd')
+
+ MarkerNamesExistedString = fd.formdata.getvalue('MarkerNamesExisted')
+ MarkerNamesAddedString = fd.formdata.getvalue('MarkerNamesAdded')
+
+ MarkerNamesExisted = []
+ MarkerNamesAdded = []
+
+ MarkerNamesExistedString = MarkerNamesExistedString.strip()
+ MarkerNamesExisted = MarkerNamesExistedString.split(',')
+
+ MarkerNamesAddedString = MarkerNamesAddedString.strip()
+ if MarkerNamesAddedString:
+ MarkerNamesAdded = MarkerNamesAddedString.split(',')
+
+ GroupNeedExport = []
+ # To simplify the business logic, just add this group to the list anyway
+ GroupNeedExport.append(InbredSetName)
+
+
+ for one_marker in MarkerNamesExisted:
+ if self.checkMarkerHasBeenInGroup(InbredSetName=InbredSetName, MarkerName=one_marker, fd=fd):
+ GroupNeedExport = self.changeMarker( InbredSetName=InbredSetName, MarkerWebID=one_marker, MarkerName=one_marker, GroupNeedExport=GroupNeedExport, fd=fd)
+
+ if MarkerNamesAdded:
+ for one_marker in MarkerNamesAdded:
+ input_name = fd.formdata.getvalue( one_marker + markerName_Feild_Separator + 'Name' )
+ GroupNeedExport = self.changeMarker( InbredSetName=InbredSetName, MarkerWebID=one_marker, MarkerName=input_name, GroupNeedExport=GroupNeedExport, fd=fd)
+
+ export_info = self.exportAllGenoFiles( GroupNeedExport )
+
+ contents = []
+
+ contents.append(export_info)
+
+ HTInput_FormId = HT.Input(type='hidden', name='FormID', value='updGeno')
+ HTInput_Back = HT.Input(type="submit", name="backButton", value="Back to main page", Class="button")
+ HTForm_Back = HT.Form(name='StrainForm', cgi=os.path.join(webqtlConfig.CGIDIR, 'main.py'), \
+ enctype= 'multipart/form-data', submit=HTInput_Back)
+ HTForm_Back.append(HTInput_FormId)
+
+ contents.append(str(HTForm_Back))
+
+ return '<BR>'.join(contents)
+
+ # return "%s" % export_info
+
+
+
+ def checkMarkerHasBeenInGroup(self, InbredSetName="", MarkerName="", fd=None):
+
+ isChanged = False
+
+ # retrive Marker information from database
+ MarkerGroupInfo = retrieveMarkerInfoForGroup (self.cursor, MarkerName, InbredSetName)
+
+ GenoId = MarkerGroupInfo[0]
+
+ GenoInfo={}
+
+ for i in range(1, len(MarkerGroupInfo)):
+ if MarkerGroupInfo[i] != None:
+ GenoInfo[MarkerInfoField[i-1]] = str( MarkerGroupInfo[i] )
+ else:
+ GenoInfo[MarkerInfoField[i-1]] = ''
+
+ if GenoInfo['Used_for_mapping'] == 'Y':
+ GenoInfo['Used_for_mapping'] = True
+ else:
+ GenoInfo['Used_for_mapping'] = False
+
+
+ # check the changing of Geno information
+
+ for i in range(0, len(MarkerInfoField)):
+
+ if MarkerInfoField[i] == 'Name':
+ continue
+
+ webInputValue = fd.formdata.getvalue( MarkerName + markerName_Feild_Separator + MarkerInfoField[i] )
+
+
+ if MarkerInfoField[i] == 'Used_for_mapping':
+ if webInputValue == 'on':
+ webInputValue = True
+ else:
+ webInputValue = False
+
+
+ if GenoInfo[MarkerInfoField[i]] != webInputValue:
+ isChanged = True
+
+ # retrive Marker alleles
+ GenoFreezeId = retrieveGenoFreezeId(self.cursor, InbredSetName)
+ db_alleles = retrieveAllele (self.cursor, GenoFreezeId, GenoId)
+ StrainList = retrieveStrainUsedForMapping (self.cursor, InbredSetName)
+
+
+ # check the changing of allele values
+
+ for i in range(0, len(StrainList)):
+ webInputValue = fd.formdata.getvalue(MarkerName + markerName_Feild_Separator + StrainList[i])
+
+ if not db_alleles.has_key(StrainList[i]):
+ #XZ: This is hard coded.
+ #XZ: The best way is to check if the input value is in ('B', 'D', 'H').
+ if webInputValue.upper() != 'X': # 'X' is the symbol for unknown allele.
+ isChanged = True
+ else:
+ if str( db_alleles[StrainList[i]]) != webInputValue:
+ isChanged = True
+
+
+ return isChanged
+
+
+ def changeMarker(self,InbredSetName="", MarkerWebID="", MarkerName="", GroupNeedExport=[], fd=None):
+
+ GenoFreezeId = retrieveGenoFreezeId( self.cursor, InbredSetName )
+
+ MarkerGroupInfo = retrieveMarkerInfoForGroup(self.cursor, MarkerName, InbredSetName)
+
+ # This marker has record for this group.
+ # Need to keep the original GeneId and marker name.
+ if MarkerGroupInfo:
+
+ #XZ: The first item of MarkerInfo is Geno.Id
+ GenoId = MarkerGroupInfo[0]
+
+ #This function should be excuted before update Chr and Mb in database.
+ GroupNeedExport = getAllGroupsNeedExported(self.cursor, GroupNeedExport=GroupNeedExport, GenoId=GenoId, \
+ Chr=fd.formdata.getvalue(MarkerWebID + markerName_Feild_Separator + 'Chr'), \
+ Mb=fd.formdata.getvalue(MarkerWebID + markerName_Feild_Separator + 'Mb') )
+
+ # Update the info in Geno (Chr, Mb, Sequence, Source).
+ updateGeno(self.cursor, GenoId, InbredSetName, MarkerWebID, fd)
+
+ # Update GenoXRef (cM, Used_for_mapping)
+ updateGenoXRef(self.cursor, GenoFreezeId, GenoId, MarkerWebID, fd)
+
+ # Keep the original GenoXRef.DataId value.
+ DataId = retrieveDataId(self.cursor, GenoId, InbredSetName)
+
+ # Delete the original alleles
+ cmd = "delete from GenoData where Id=%s" % DataId
+ self.cursor.execute(cmd)
+
+ # Insert new alleles.
+ insertGenoData(cursor=self.cursor, InbredSetName=InbredSetName, DataId=DataId, MarkerWebID=MarkerWebID, fd=fd)
+
+ else: # No record for this group.
+
+ hasInfoForSpecies = checkIfMarkerInSpecies(self.cursor, MarkerName, InbredSetName)
+
+ if hasInfoForSpecies:
+
+ # Keep the original GenoId.
+ GenoId = hasInfoForSpecies[0]
+
+ #This function should be excuted before update Chr and Mb in database.
+ GroupNeedExport = getAllGroupsNeedExported(self.cursor, GroupNeedExport=GroupNeedExport, GenoId=GenoId, \
+ Chr=fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Chr' ), \
+ Mb=fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Mb') )
+
+
+ # Update the info in Geno (Chr, Mb, Sequence, Source).
+ updateGeno(self.cursor, GenoId, InbredSetName, MarkerWebID, fd)
+
+
+ # Get new GenoData.Id
+ DataId = retrieveMaxGenoDataId(self.cursor) + 1
+
+ # Add record in GenoXRef table for this group.
+ addGenoXRef(self.cursor, GenoFreezeId, GenoId, DataId, MarkerWebID, fd)
+
+ # Add record in GenoData table.
+ insertGenoData(cursor=self.cursor, InbredSetName=InbredSetName, DataId=DataId, MarkerWebID=MarkerWebID, fd=fd)
+
+ else:
+ # Get new Geno.Id
+ GenoId = retrieveMaxGenoId(cursor=self.cursor) + 1
+
+ # Add record in Geno
+ addGeno(self.cursor, GenoId, InbredSetName, MarkerWebID, fd)
+
+ # Get new GenoData.Id
+ DataId = retrieveMaxGenoDataId(self.cursor) + 1
+
+ # Add record into GenoXRef table.
+ addGenoXRef(self.cursor, GenoFreezeId, GenoId, DataId, MarkerWebID, fd)
+
+ #Add record into GenoData table.
+ insertGenoData(cursor=self.cursor, InbredSetName=InbredSetName, DataId=DataId, MarkerWebID=MarkerWebID, fd=fd)
+
+ return GroupNeedExport
+
+
+
+ def exportAllGenoFiles (self, InbredSetNameList = []):
+
+ warning = "As to the change made, the following groups need to be exported to generate new geno files: %s\n<br><br> " % str(InbredSetNameList)
+
+ whiteList = ['BXD']
+
+ warning = warning + "At current development stage, the following groups can be exported to generate geno files: %s\n<br><br>" % str(whiteList)
+ warning = warning + "Here are the geno files that are ACTUALLY exported according to the change you made:\n<br>"
+
+ blackList = []
+ for one_group in InbredSetNameList:
+ if one_group in whiteList:
+ self.exportOneGenoFile( one_group )
+ warning = warning + "<a href='/genotypes/%s.geno" % one_group + "'>" + one_group + " geno file</a>\n<br>"
+ else:
+ blackList.append(one_group)
+
+ return warning
+
+
+
+ def exportOneGenoFile (self, InbredSetName=''):
+
+ geno_file = open(webqtlConfig.GENODIR + InbredSetName + '.geno', 'w')
+
+ query = "select SpeciesId from InbredSet where Name='%s' " % InbredSetName
+ self.cursor.execute( query )
+ SpeciesId = self.cursor.fetchone()[0]
+
+ GenoFreezeId = retrieveGenoFreezeId( self.cursor, InbredSetName )
+
+ StrainUsedForMapping = retrieveStrainUsedForMapping(self.cursor, InbredSetName )
+
+ StrainNameIdUsedForMapping = retrieveStrainNameIdUsedForMapping( self.cursor, InbredSetName )
+
+ GenoCode_record = retrieveGenoCode(self.cursor, InbredSetName )
+
+ Allle_value_symbol = {}
+ symbol_for_unknown = ''
+
+ for one_result in GenoCode_record:
+ if str(one_result[2]) != 'None':
+ Allle_value_symbol[one_result[2]] = one_result[1]
+ else:
+ symbol_for_unknown = one_result[1]
+
+
+ geno_file.write('@name:%s\n' % InbredSetName )
+
+ GeneticType = retrieveGeneticTypeOfInbredSet(self.cursor, InbredSetName )
+
+ geno_file.write('@type:%s\n' % str(GeneticType) )
+
+ for one_result in GenoCode_record:
+ geno_file.write('@%s:%s\n' % (one_result[0], one_result[1]) )
+
+ geno_file.write('Chr\tLocus\tcM\tMb')
+
+ for one_strain in StrainUsedForMapping:
+ geno_file.write('\t%s' % one_strain )
+
+
+ query = "select Geno.Chr, Geno.Name, GenoXRef.cM, Geno.Mb, GenoXRef.DataId from Geno, GenoXRef where SpeciesId=%s and GenoFreezeId=%s and Used_for_mapping='Y' and Geno.Id=GenoId order by chr_num, Mb" % (SpeciesId, GenoFreezeId)
+ self.cursor.execute( query )
+ results = self.cursor.fetchall()
+
+ StrainId_Allele = {}
+
+ for one_result in results:
+ Chr, Name, cM, Mb, DataId = one_result
+ geno_file.write('\n%s\t%s\t%s\t%s' % (Chr, Name, cM, Mb) )
+
+ StrainId_Allele = {}
+
+ query = "select StrainId, value from GenoData where Id=%s " % DataId
+ self.cursor.execute( query )
+ GenoData_results = self.cursor.fetchall()
+
+ for one_GenoData_result in GenoData_results:
+ StrainId_Allele[ one_GenoData_result[0] ] = one_GenoData_result[1]
+
+ for one_strain_name in StrainUsedForMapping:
+ one_strain_id = StrainNameIdUsedForMapping[ one_strain_name ]
+
+ if StrainId_Allele.has_key( one_strain_id ):
+ one_allele_value = StrainId_Allele[one_strain_id]
+ one_allele_symbol = Allle_value_symbol[ one_allele_value ]
+ geno_file.write( '\t%s' % one_allele_symbol )
+ else:
+ geno_file.write( '\t%s' % symbol_for_unknown )
+
+
+
+
+
+
+
+
+
+
+
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 19:45:52 +0000