def __pslCheck(self):
"""Runs pslCheck program on this table and sends result to reporter's filehandle."""
self.reporter.beginStep(self.db, self.table, "pslCheck")
# Get baseColorUseSequence setting
tdbCommand = ["tdbQuery", "select baseColorUseSequence from " + self.db +\
" where track='" + self.table +"' or table='"+ self.table +"'"]
tdbOut, tdbErr = qaUtils.runCommand(tdbCommand)
# Turn tdbOut into array so we can extract different pieces
tdbOut = tdbOut.replace("\n", "")
tdbOut = tdbOut.split(" ")
# tdbOut[1] should be what option is used for baseColorUseSequence
# We want to fully run pslCheck for those entries with "table" and "extFile"
if len(tdbOut) > 2:
if tdbOut[1] == "table":
# Get sizes of sequences in specified table
sizesOut = qaUtils.callHgsql(
self.db, "select name, length(seq) from " + tdbOut[2])
elif tdbOut[1] == "extFile":
# Extract sizes from named seq table
sizesOut = qaUtils.callHgsql(
self.db, "select acc, size from " + tdbOut[2])
# Write itemSizes to file
itemSizes = open("%s.sizes" % self.table, 'w')
itemSizes.write(sizesOut)
itemSizes.close()
# Check if $db.sizes file exists
if not os.path.isfile("%s.chrom.sizes" % self.db):
# If it doens't exist, get chrom sizes from chromInfo
chromSizesOut = qaUtils.callHgsql(self.db,
"select * from chromInfo")
chromSizes = open("%s.chrom.sizes" % self.db, 'w')
chromSizes.write(chromSizesOut)
chromSizes.close()
# Run more in-depth version of pslCheck
command = ("pslCheck", "-querySizes=%s.sizes" % self.table ,\
"-targetSizes=%s.chrom.sizes" % self.db, "-db=" + self.db, self.table)
self.reporter.writeCommand(command)
commandOut, commandErr, commandReturnCode = qaUtils.runCommandNoAbort(
command)
# Write output to file
self.reporter.fh.write(commandErr)
# Clean up intermediate item sizes file
os.remove("%s.sizes" % self.table)
# For everything else, use generic set of steps
else:
command = ["pslCheck", "db=" + self.db, self.table]
self.reporter.writeCommand(command)
commandOut, commandErr, commandReturnCode = qaUtils.runCommandNoAbort(
command)
self.reporter.fh.write(commandErr)
if commandReturnCode:
self.recordError()
else:
self.recordPass()
self.reporter.endStep()
def __pslCheck(self):
"""Runs pslCheck program on this table and sends result to reporter's filehandle."""
self.reporter.beginStep(self.db, self.table, "pslCheck")
# Get baseColorUseSequence setting
tdbCommand = ["tdbQuery", "select baseColorUseSequence from " + self.db +\
" where track='" + self.table +"' or table='"+ self.table +"'"]
tdbOut, tdbErr = qaUtils.runCommand(tdbCommand)
# Turn tdbOut into array so we can extract different pieces
tdbOut = tdbOut.replace("\n","")
tdbOut = tdbOut.split(" ")
# tdbOut[1] should be what option is used for baseColorUseSequence
# We want to fully run pslCheck for those entries with "table" and "extFile"
if len(tdbOut) > 2:
if tdbOut[1] == "table":
# Get sizes of sequences in specified table
sizesOut = qaUtils.callHgsql(self.db, "select name, length(seq) from " + tdbOut[2])
elif tdbOut[1] == "extFile":
# Extract sizes from named seq table
sizesOut = qaUtils.callHgsql(self.db, "select acc, size from " + tdbOut[2])
# Write itemSizes to tempfile
itemSizesTemp = tempfile.NamedTemporaryFile(mode='w')
itemSizes = open(itemSizesTemp.name, 'w')
itemSizes.write(sizesOut)
itemSizes.close()
# Write chromSizes to tempfile
chromSizesTemp = tempfile.NamedTemporaryFile(mode='w')
chromSizesOut = qaUtils.callHgsql(self.db, "select chrom,size from chromInfo")
chromSizes = open(chromSizesTemp.name, 'w')
chromSizes.write(chromSizesOut)
chromSizes.close()
# Run more in-depth version of pslCheck
command = ("pslCheck", "-querySizes=" + itemSizesTemp.name ,\
"-targetSizes=" + chromSizesTemp.name, "-db=" + self.db, self.table)
self.reporter.writeCommand(command)
commandOut, commandErr, commandReturnCode = qaUtils.runCommandNoAbort(command)
# Write output to file
self.reporter.fh.write(commandErr)
# For everything else, use generic set of steps
else:
command = ["pslCheck", "db=" + self.db, self.table]
self.reporter.writeCommand(command)
commandOut, commandErr, commandReturnCode = qaUtils.runCommandNoAbort(command)
self.reporter.fh.write(commandErr)
if commandReturnCode:
self.recordError()
else:
self.recordPass()
self.reporter.endStep()
def __checkTableCoords(self):
"""Runs checkTableCoords program on this table."""
self.reporter.beginStep(self.db, self.table, "checkTableCoords")
command = ["checkTableCoords", self.db, self.table]
self.reporter.writeCommand(command)
commandOut, commandErr, commandReturnCode = qaUtils.runCommandNoAbort(command)
self.reporter.fh.write(commandErr)
if commandReturnCode:
self.recordError()
else:
self.recordPass()
self.reporter.endStep()
def __genePredCheck(self):
"""Runs genePredCheck program on this table and sends results to reporter's filehandle."""
self.reporter.beginStep(self.db, self.table, "genePredCheck")
command = ["genePredCheck", "db=" + self.db, self.table]
self.reporter.writeCommand(command)
commandOut, commandErr, commandReturnCode = qaUtils.runCommandNoAbort(command)
self.reporter.fh.write(commandErr)
if commandReturnCode:
self.recordError()
else:
self.recordPass()
self.reporter.endStep()
def __positionalTblCheck(self):
"""Runs positionalTblCheck program on this table. Excludes GenBank tables."""
if not self.__isGenbankTable():
self.reporter.beginStep(self.db, self.table, "positionalTblCheck")
command = ["positionalTblCheck", self.db, self.table]
self.reporter.writeCommand(command)
commandOut, commandErr, commandReturnCode = qaUtils.runCommandNoAbort(command)
self.reporter.fh.write(commandErr)
if commandReturnCode:
self.recordError()
else:
self.recordPass()
self.reporter.endStep()
def __genePredCheck(self):
"""Runs genePredCheck program on this table and sends results to reporter's filehandle."""
self.reporter.beginStep(self.db, self.table, "genePredCheck")
command = ["genePredCheck", "db=" + self.db, self.table]
self.reporter.writeCommand(command)
commandOut, commandErr, commandReturnCode = qaUtils.runCommandNoAbort(
command)
self.reporter.fh.write(commandErr)
if commandReturnCode:
self.recordError()
else:
self.recordPass()
self.reporter.endStep()
def getTrackType(db, track):
"""Looks for a track type via tdbQuery."""
cmd = ["tdbQuery", "select type from " + db + " where track='" + track +
"' or table='" + track + "'"]
cmdout, cmderr, cmdreturncode = qaUtils.runCommandNoAbort(cmd)
if cmdreturncode != 0:
# keep command arguments nicely quoted
cmdstr = " ".join([pipes.quote(arg) for arg in cmd])
raise Exception("Error from: " + cmdstr + ": " + cmderr)
if cmdout:
trackType = cmdout.split()[1]
else:
trackType = None
return trackType
def getTrackType(db, table):
"""Looks for a track type via tdbQuery."""
cmd = [
"tdbQuery", "select type from " + db + " where track='" + table +
"' or table='" + table + "'"
]
cmdout, cmderr, cmdreturncode = qaUtils.runCommandNoAbort(cmd)
if cmdreturncode != 0:
# keep command arguments nicely quoted
cmdstr = " ".join([pipes.quote(arg) for arg in cmd])
raise Exception("Error from: " + cmdstr + ": " + cmderr)
if cmdout:
tableType = cmdout.split()[1]
else:
tableType = None
return tableType