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#!/usr/bin/python
"""
document the protocol
"""
import os, sys, subprocess, logging, time
from optparse import OptionParser
from string import Template
from xml.etree import ElementTree
from glob import glob
STAGES = ["setup", "mapping", "support", "extraction", "assembly", "output"]
from pbsuite.jelly import Stages
from pbsuite.utils.setupLogging import *
from pbsuite.utils.CommandRunner import *
USAGE = """USAGE: Jelly.py <stage> <protocol.xml> [-x \"--options for stage\"]
Jelly is the driver for each stage of the
reference genome upgrade.
<stage> is one of
%s
<protocol.xml> contains the information about the
data and parameters Jelly will run. See README.txt
or the documentation for the Protocol's format.""" % ("\n\t".join(STAGES))
class JellyProtocol():
"""
Independent method to parse protocols
"""
def __init__(self, fileName):
self.protocolName = os.path.abspath(fileName)
self.parseProtocol()
def parseProtocol(self):
"""
Parses a Jelly Protocol
"""
try:
file = ElementTree.parse(self.protocolName)
except Exception:
logging.error(("If you're actually sure the input Protocol is "\
"where you said it is, then the Protocol doesn't "\
"have valid XML Format. Use an XML validator."))
sys.exit(1)
root = file.getroot()
refNode = root.find("reference")
if refNode is None:
logging.error("Protocol doesn't have <reference> element.")
sys.exit(1)
else:
self.scaffoldName = refNode.text
if not os.path.exists(self.scaffoldName):
logging.error("Reference %s Does Not Exist!" % (self.scaffoldName))
sys.exit(1)
self.referenceNameBase = self.scaffoldName[:self.scaffoldName.rindex(".fasta")]
self.scaffoldQualName = self.referenceNameBase+".qual"
if not os.path.exists(self.scaffoldQualName):
sys.stderr.write(("[WARNING] Couldn't find %s... assuming there " \
"isn't a quality file for the reference\n") % \
(self.scaffoldQualName))
self.scaffoldQualName = None
self.gapTable = self.referenceNameBase+".gapInfo.bed"
self.reference = self.scaffoldName
self.referenceIndex = self.reference+".sa"
inputNode = root.find("input")
if inputNode.attrib.has_key("baseDir"):
self.baseDir = inputNode.attrib["baseDir"]
else:
self.baseDir = ""
self.inputs = []
for input in inputNode:
#Do some checking on the inputs
fullPath = os.path.join(self.baseDir, input.text)
if not os.path.exists(fullPath):
logging.error("Input %s doesn't exit! Exiting" % (fullPath))
exit(0)
if not (fullPath.lower().endswith('.fasta') or fullPath.lower().endswith('.fastq')):
logging.error("Input %s needs to end with .fasta or .fastq! Exiting" % (fullPath))
exit(0)
self.inputs.append(fullPath)
if len(self.inputs) == 0:
logging.error("Protocol doesn't specifiy any input inputs!")
sys.exit(1)
outputNode = root.find("outputDir")
if outputNode is None:
logging.warning("Output directory not specified. Using pwd. Hope you're cool with that...")
self.outDir = os.getcwd()
else:
self.outDir = outputNode.text
#Command Runner is going to sort all this out.
#And create an object to do the calls.
self.runXML = root.find("cluster")
blasrNode = root.find("blasr")
if blasrNode is None:
logging.warning("No blasr parameters!?")
self.blasrParams = ""
else:
self.blasrParams = blasrNode.text
class JellyRunner():
"""
Take a JellyProtocol and loads in the variables in a way that
JellyRunner can use it easily!
"""
def __init__(self):
"""
Given a protocol fn, load it up so we are ready to run.
"""
self.parseArgs()
setupLogging(self.options.debug)
sys.stderr.write("""
Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
Gap: Upgrading Genomes with Pacific Biosciences RS
Long-Read Sequencing Technology." PLoS ONE 7, no. 11
(November 21, 2012): e47768.
doi:10.1371/journal.pone.0047768.\n\n""")
self.parseProtocol()
def parseProtocol(self):
self.protocol = JellyProtocol(self.protocolName)
self.parseCluster(self.protocol.runXML)
def parseCluster(self, xmlNode):
if xmlNode is None:
self.runCmd = CommandRunner()
else:
command = xmlNode.find("command")
if command is None:
logging.error(("You're trying to use a cluster " \
"template, but you didn't specify the " \
"template. Please read the documentation." \
"Exiting.\n"""))
sys.exit(1)
nJobs = xmlNode.find("nJobs")
if nJobs is None or nJobs.text == '0':
logging.warning(("Not Specifying number of jobs may " \
"overload clusters."))
nJobs = 0
else:
nJobs = int(nJobs.text)
cmdTemplate = command.text
self.runCmd = CommandRunner(cmdTemplate, nJobs)
def parseArgs(self):
"""
Uses OptionParser to parse out input
Jelly.py <stage> <protocol>
"""
parser = OptionParser(USAGE)
parser.remove_option("-h")
parser.add_option("-h", "--help", action="store_true", default=False)
parser.add_option("--debug",action="store_true",default=False)
parser.add_option("-x", dest="extras", type="string", default="",
help="-x \"<options>\" are options to pass into the stage you're running")
self.options, args = parser.parse_args()
if self.options.help == True:
if len(args) == 1:
if args[0] in STAGES:
print exe(Stages.PRINT_HELPS[args[0]])[1]
sys.exit(0)
#Else, this will drop down to the next parser.error
else:
print parser.format_help()
sys.exit(0)
if len(args) != 2 or args[0] not in STAGES:
parser.error("Invalid Arguments. Expected one of\n'%s'" % "', '".join(STAGES))
sys.exit(1)
self.executeStage = args[0]
self.protocolName = os.path.abspath(args[1])
def run(self):
logging.info("Executing Stage: %s" % self.executeStage)
if self.options.debug:
Stages.DEBUG = "--debug"
#Setup before a stage and run
if self.executeStage == "setup":
wDir = os.path.dirname(self.protocol.scaffoldName)
myCommands = [Stages.setup(self.protocol.scaffoldName, \
self.protocol.scaffoldQualName, self.protocol.gapTable, \
self.options.extras)]
elif self.executeStage == "mapping":
wDir = os.path.join(self.protocol.outDir, "mapping")
try:
os.mkdir(wDir)
except OSError:
logging.debug("%s already exists" % wDir)
if not os.path.exists(wDir):
logging.warning("%s was not created. Check write permissions!" % wDir)
sys.exit(1)
myCommands = Stages.mapping(self.protocol.inputs, wDir, \
self.protocol.reference, self.protocol.referenceIndex, \
self.protocol.blasrParams, self.options.extras)
elif self.executeStage == "support":
wDir = os.path.join(self.protocol.outDir, "support")
try:
os.mkdir(wDir)
except OSError:
logging.debug("%s already exists" % wDir)
if not os.path.exists(wDir):
logging.warning("%s was not created. Check write permissions!" % wDir)
sys.exit(1)
myCommands = Stages.support(self.protocol.outDir, self.protocol.gapTable, \
wDir, self.options.extras)
elif self.executeStage == "extraction":
wDir = os.path.join(self.protocol.outDir, "assembly")
try:
os.mkdir(wDir)
except OSError:
logging.debug("%s already exists" % wDir)
if not os.path.exists(wDir):
logging.warning("%s was not created. Check write permissions!" % wDir)
sys.exit(1)
myCommands = [Stages.extraction(wDir, \
self.protocolName, \
self.options.extras)]
elif self.executeStage == "assembly":
wDir = os.path.join(self.protocol.outDir, "assembly")
myCommands = Stages.assembly(wDir, self.protocol.gapTable, \
self.options.extras)
elif self.executeStage == "output":
wDir = os.path.join(self.protocol.outDir, "assembly")
myCommands = [Stages.collection(self.protocol.outDir, self.protocol, self.options.extras)]
logging.debug("CommandRunner Returned: " +
str(self.runCmd(myCommands, wDir, self.executeStage )) )
logging.info("Finished %s Stage: %s" % (self.runCmd.runType, self.executeStage))
if __name__ == '__main__':
prog = JellyRunner()
prog.run()
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