def getHitsForPrimary():
'''
Selects appropriate row from primaryTable, and updates domains
to include the one from HMMERSearch
'''
print "adding domains to primary table"
# get gis from primary table
giList = databaseMethods.databaseRows(databaseName, primaryTable)
# check hit id (gi) is in giList
for hit in queryResult:
if hit.id in giList:
# get domains from gi row in primary table
domainString = databaseMethods.getGIRow(databaseName, primaryTable, hit.id)
# add the domain
domainString2 = domainString + "|" + str(queryResult.id)
# replace into primary table
databaseMethods.updateDomains(databaseName, primaryTable, domainString2, hit.id)
else:
# send warning message
warnings.warn("Notice: gi %s is not in primary table." % hit.id)
def getHitsForPrimary():
'''
Selects appropriate row from primaryTable, and updates domains
to include the one from HMMERSearch
'''
print "adding domains to primary table"
# get gis from primary table
giList = databaseMethods.databaseRows(databaseName, primaryTable)
# check hit id (gi) is in giList
for hit in queryResult:
if hit.id in giList:
# get domains from gi row in primary table
domainString = databaseMethods.getGIRow(databaseName, primaryTable,
hit.id)
# add the domain
domainString2 = domainString + "|" + str(queryResult.id)
# replace into primary table
databaseMethods.updateDomains(databaseName, primaryTable,
domainString2, hit.id)
else:
# send warning message
warnings.warn("Notice: gi %s is not in primary table." % hit.id)
A helper function to insert information into the *domain* table.
'''
# collect info needed to insert into domains table
domainInfo = [(hitInfo["gi"], hitInfo["domain"], hitInfo["start"], \
hitInfo["end"], hitInfo["sequence"], hitInfo["score"])]
# insert into domains db
databaseMethods.domainDatabaseInsert(domainInfo, databaseName, domainTable)
def insertPrimary(domain, giVal):
'''
A helper function to insert information into the *primary* table.
'''
gi = giVal.split("_")[0]
if gi in giList:
# update domains in primary table
databaseMethods.concatDomains(databaseName, primaryTable, query, gi)
else:
# send warning message
warnings.warn("Notice: gi %s is not in primary table." % gi)
# ----------------CALLS-----------------------------------
# get information out of jackhmmer file
jackHmmerInfo = jackhmmerParse.jackhmmerParse(query, jackhmmerFile)
# length of jackHMMER info
lenJackHmmer = len(jackHmmerInfo)
# get list of gis from primary table
giList = databaseMethods.databaseRows(databaseName, primaryTable)
# run through every hit in jackHmmerInfo
loopHits(jackHmmerInfo)
'''
# collect info needed to insert into domains table
domainInfo = [(hitInfo["gi"], hitInfo["domain"], hitInfo["start"], \
hitInfo["end"], hitInfo["sequence"], hitInfo["score"])]
# insert into domains db
databaseMethods.domainDatabaseInsert(domainInfo, databaseName, domainTable)
def insertPrimary(domain, giVal):
'''
A helper function to insert information into the *primary* table.
'''
gi = giVal.split("_")[0]
if gi in giList:
# update domains in primary table
databaseMethods.concatDomains(databaseName, primaryTable, query, gi)
else:
# send warning message
warnings.warn("Notice: gi %s is not in primary table." % gi)
# ----------------CALLS-----------------------------------
# get information out of jackhmmer file
jackHmmerInfo = jackhmmerParse.jackhmmerParse(query, jackhmmerFile)
# length of jackHMMER info
lenJackHmmer = len(jackHmmerInfo)
# get list of gis from primary table
giList = databaseMethods.databaseRows(databaseName, primaryTable)
# run through every hit in jackHmmerInfo
loopHits(jackHmmerInfo)