P_Control.py Disable task (which calls summarizeCompareByMovie.py) to handle expired SMRT Cell lots.

Notes.md

Updating 2.1

Replace $SEYMOUR_HOME/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/modules/P_Control.py in SMRTAnalysis 2.1.

P_Control.py

#
# $Id: //depot/branches/springfield/S2.1/software/assembly/pbpy/pbpy/smrtpipe/modules/P_Control.py#1 $
#
"""
v1.0 version of a module which aligns a set of reads to a spike-in control
sequence.
"""
import os
import logging

from pbpy.io.ReferenceEntry import ReferenceEntry
from pbpy.smrtpipe.engine.SmrtPipeTasks import task
from pbpy.smrtpipe.engine.DistributableTasks import DistributableTask
from pbpy.smrtpipe.modules.P_Aligner import P_Aligner
from pbpy.smrtpipe.engine.SmrtPipeFiles import (SMRTDataFile, MovieFOFN,
                                                verifySyncedFofn)
from pbpy.smrtpipe.modules.P_Fetch import inputPlsFofn
from pbpy.smrtpipe.engine.common import USE_GLOBAL_NPROC
from pbpy.smrtpipe.cluster.Scatter import ScatterFofn, NoOpScatter
from pbpy.smrtpipe.cluster.Gather import GatherCmpH5, GatherSyncedFofn
from pbpy.smrtpipe.modules.P_Filter import filteredRgnFofn
from pbpy.smrtpipe.core.utils import toSmrtVersion

## Generated by P_Control ###################################################
#
# Before defining the module we define the set of 
# files created by the tasks in this module.
#
controlCmpH5        = SMRTDataFile("data/control_reads.cmp.h5",
                                   group        = "Diagnostic",
                                    dataItem     = "Control Reads",
                                    format       = "cmp.h5")
#
noControlRgnFofn    = MovieFOFN("data/post_control_regions.fofn")
noControlRgnFofn.addVerifyFunction( verifySyncedFofn( inputPlsFofn ) )

controlSummaryCSV   = SMRTDataFile("data/control_results_by_movie.csv",
                                   group        = "Diagnostic",
                                    dataItem     = "Control Summary",
                                    format       = "csv")

log = logging.getLogger(__name__)

_MAJOR_VERSION = "2.2"
_rev = "$Revision: #1 $"
_version = "$Change: 127046 $"
__version__ = toSmrtVersion(_MAJOR_VERSION, _version)


class P_Control( P_Aligner ):
    """Will align a set of reads to a spike-in control sequence and output them
    as contigs."""

    VERSION = __version__

    def validateSettings( self ):
        """Extract relevant settings from the context and store as attributes
        of this module, setting defaults and validating where necessary."""
        
        errors = P_Aligner.validateSettings( self )
        
        self.reentrant = True

        self.pbinternal = self.setting('pbinternal', 'False')
        
        # for unrolled control sequences we need to mandate aligning the
        # whole read (not the subreads)
        # (this might change if we ever switch to library-based controls)
        self.useSubreads = False
        self.filterAdapterOnly = True

        # Validate the spike-in control reference
        if 'control' in self._context:
            self.refFile = self._context.getFile('control')

            if not os.path.exists(self.refFile):
                errors.append("Can't find spike-in control file %s" % self.refFile)

            self.reference = ReferenceEntry(self.refFile)
        else:
            msg = "DISABLING {c} module and all tasks in {c}. No control sequence identifier specified (parameter 'global.control')"
            log.warning(msg.format(c=self.__class__.__name__))
            self.disableTasks()
        return errors

    # 
    # The nproc parameter controls how many processors/slots will be reserved for
    # each instance of this task in a Distributed setting. The value USE_GLOBAL_NPROC 
    # will use the value set in smrtpipe.rc.
    #
    # When specifying inputs, a tuple of files will be resolved when the initial
    # graph is created. The tuple is resolved to the left-most file in the tuple
    # that is generated by another task in the graph. For example, in the align task
    # below, 'rgnFofn' will resolve to filteredRgnFofn if P_Filter is run, otherwise
    # it will default to inputPlsFofn.
    #
    @task( inputs   = { 'plsFofn'   : inputPlsFofn,
                        'rgnFofn'   : ( filteredRgnFofn, inputPlsFofn ) },
           outputs  = { 'cmpH5'     : controlCmpH5 },
           nproc    = USE_GLOBAL_NPROC,
           taskType = DistributableTask,
           scatters = [ ScatterFofn( inputPlsFofn ), 
                        ScatterFofn(( filteredRgnFofn, inputPlsFofn )) ],
           gathers  = [ GatherCmpH5( controlCmpH5 ) ] )
    def align( self, files ):
        return ( self._align( files ), 
                "echo 'Alignment Complete'", "date", 
                self._loadPulses( files ) )
    #
    # In some cases the tasks can be engineered such that a scatter
    # or gather will never be run. In that case, feel free to make
    # use of the provided NoOpScatter and NoOpGather.
    #
    @task( inputs   = { 'cmpH5'     : controlCmpH5,
                        'rgnFofn'   : ( filteredRgnFofn, inputPlsFofn ) },
           outputs  = { 'noCtrlFofn': noControlRgnFofn },
           taskType = DistributableTask,
           scatters = [ ScatterFofn(( filteredRgnFofn, inputPlsFofn )), 
                        NoOpScatter( controlCmpH5 ) ],
           gathers  = [ GatherSyncedFofn( noControlRgnFofn, inputPlsFofn ) ] )
    def updateRgn( self, files ):
        """Pass forward the information required to ignore control reads in the downstream alignment."""
        return "maskAlignedReads.py %s %s %s" % \
                ( files.cmpH5.path, files.rgnFofn.path, files.noCtrlFofn.path )

    @task( inputs   = { 'plsFofn'   : inputPlsFofn,
                        'cmpH5wP'   : controlCmpH5 },
           outputs  = { 'summary'   : controlSummaryCSV },
           enabled=False )
    def summaryCSV( self, files ):
        """Write out a CSV file summarizing the control alignment results."""
        extOpt = '--external' if not self.pbinternal else ''
        return 'summarizeCompareByMovie.py %s --fofn=%s %s > %s' % \
                    ( extOpt, files.plsFofn.path, files.cmpH5wP.path, files.summary.path )