comparison rlGAT/gat-run.py @ 11:53487f21c0d5 draft

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################################################################################
#
#   MRC FGU Computational Genomics Group
#
#   $Id: script_template.py 2871 2010-03-03 10:20:44Z andreas $
#
#   Copyright (C) 2009 Andreas Heger
#
#   This program is free software; you can redistribute it and/or
#   modify it under the terms of the GNU General Public License
#   as published by the Free Software Foundation; either version 2
#   of the License, or (at your option) any later version.
#
#   This program is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.
#
#   You should have received a copy of the GNU General Public License
#   along with this program; if not, write to the Free Software
#   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
#################################################################################
'''
gat-run - run the genomic annotation tool
=============================================

:Author: Andreas Heger
:Release: $Id$
:Date: |today|
:Tags: Python

Purpose
-------

This script compares one or more genomic segments of interest 
against one more other genomic annotations.

Usage
-----

Example::

   python gat-run.py 
      --segment-file=segments.bed.gz 
      --workspace-file=workspace.bed.gz 
      --annotation-file=annotations_architecture.bed.gz  
 
Type::

   python gat-run.py --help

for command line help.

Documentation
-------------

Code
----

'''

import os, sys, re, optparse, collections, types, glob, time
import numpy

import gat
import gat.Experiment as E
import gat.IOTools as IOTools
import gat.IO as IO
import gat.Stats as Stats
import GatSegmentList
import GatEngine

def fromSegments( options, args ):
    '''run analysis from segment files. 

    This is the most common use case.
    '''

    tstart = time.time()

    ##################################################
    ##################################################
    ##################################################
    ## build segments
    segments, annotations, workspaces, isochores = IO.buildSegments( options )

    E.info( "intervals loaded in %i seconds" % (time.time() - tstart) )

    ##################################################
    ##################################################
    ##################################################
    ## open various additional output files
    ##################################################
    outfiles = {}
    for section in ("sample", 
                    "segment_metrics",
                    "sample_metrics",
                    ):
        if section in options.output_stats or \
            "all" in options.output_stats or \
                len( [ x for x in options.output_stats if re.search( x, "section" ) ] ) > 0:
            outfiles[section] = E.openOutputFile(section)

    if 'sample_metrics' in outfiles:
        outfiles['sample_metrics'].write( "track\tsection\tmetric\t%s\n" % "\t".join(Stats.Summary().getHeaders() ))

    # filter segments by workspace
    workspace = IO.applyIsochores( segments, 
                                   annotations, 
                                   workspaces,
                                   options, 
                                   isochores,
                                   truncate_segments_to_workspace = options.truncate_segments_to_workspace,
                                   truncate_workspace_to_annotations = options.truncate_workspace_to_annotations,
                                   restrict_workspace = options.restrict_workspace )

    ##################################################
    ##################################################
    ##################################################
    ## check memory requirements
    counts = segments.countsPerTrack() 
    max_counts = max(counts.values())
    # previous algorithm: memory requirements if all samples are stored
    memory = 8 * 2 * options.num_samples * max_counts * len(workspace)

    ##################################################
    ##################################################
    ##################################################
    # initialize sampler
    if options.sampler == "annotator":
        sampler = GatEngine.SamplerAnnotator(
            bucket_size = options.bucket_size,
            nbuckets = options.nbuckets )
    elif options.sampler == "shift":
        sampler = GatEngine.SamplerShift( 
            radius = options.shift_expansion,
            extension = options.shift_extension )
    elif options.sampler == "segments":
        sampler = GatEngine.SamplerSegments()
    elif options.sampler == "local-permutation":
        sampler = GatEngine.SamplerLocalPermutation()
    elif options.sampler == "global-permutation":
        sampler = GatEngine.SamplerGlobalPermutation()
    elif options.sampler == "brute-force":
        sampler = GatEngine.SamplerBruteForce()
    elif options.sampler == "uniform":
        sampler = GatEngine.SamplerUniform()
        
    ##################################################
    ##################################################
    ##################################################
    # initialize counter
    counters = []
    for counter in options.counters:
        if counter == "nucleotide-overlap":
            counters.append( GatEngine.CounterNucleotideOverlap() )
        elif counter == "nucleotide-density":
            counters.append( GatEngine.CounterNucleotideDensity() )
        elif counter == "segment-overlap":
            counters.append( GatEngine.CounterSegmentOverlap() )
        elif counter == "annotations-overlap":
            counters.append( GatEngine.CounterAnnotationsOverlap() )
        elif counter == "segment-midoverlap":
            counters.append( GatEngine.CounterSegmentMidpointOverlap() )
        elif counter == "annotations-midoverlap":
            counters.append( GatEngine.CounterAnnotationsMidpointOverlap() )
        else:
            raise ValueError("unknown counter '%s'" % counter )

    ##################################################
    ##################################################
    ##################################################
    ## initialize workspace generator
    if options.conditional == "unconditional":
        workspace_generator = GatEngine.UnconditionalWorkspace()
    elif options.conditional == "cooccurance":
        workspace_generator = GatEngine.ConditionalWorkspaceCooccurance()
    elif options.conditional == "annotation-centered":
        if options.conditional_extension == options.conditional_expansion == None:
            raise ValueError( "please specify either --conditional-expansion or --conditional-extension" )
        workspace_generator = GatEngine.ConditionalWorkspaceAnnotationCentered( options.conditional_extension,
                                                                          options.conditional_expansion )
    elif options.conditional == "segment-centered":
        if options.conditional_extension == options.conditional_expansion == None:
            raise ValueError( "please specify either --conditional-expansion or --conditional-extension" )

        workspace_generator = GatEngine.ConditionalWorkspaceSegmentCentered( options.conditional_extension,
                                                                       options.conditional_expansion )
    else:
        raise ValueError("unknown conditional workspace '%s'" % options.conditional )


    ##################################################
    ##################################################
    ##################################################
    ## check if reference is compplete
    ##################################################
    if options.reference:
        reference = options.reference
        for track in segments.tracks:
            if track not in options.reference:
                raise ValueError("missing track '%s' in reference" % track )
            r = options.reference[track]
            for annotation in annotations.tracks:
                if annotation not in r:
                    raise ValueError("missing annotation '%s' in annotations for track='%s'" % (annotation, track ))


    ##################################################
    ##################################################
    ##################################################
    ## compute
    ##################################################
    annotator_results = gat.run( segments, 
                                 annotations, 
                                 workspace,
                                 sampler, 
                                 counters,
                                 workspace_generator = workspace_generator,
                                 num_samples = options.num_samples,
                                 cache = options.cache,
                                 outfiles = outfiles,
                                 output_counts_pattern = options.output_counts_pattern,
                                 output_samples_pattern = options.output_samples_pattern,
                                 sample_files = options.sample_files,
                                 conditional = options.conditional,
                                 conditional_extension = options.conditional_extension,
                                 reference = options.reference,
                                 pseudo_count = options.pseudo_count,
                                 num_threads = options.num_threads )

    return annotator_results


def main( argv = None ):
    """script main.

    parses command line options in sys.argv, unless *argv* is given.
    """

    if not argv: argv = sys.argv

    parser = gat.buildParser( usage = globals()["__doc__"] )

    ## add common options (-h/--help, ...) and parse command line 
    (options, args) = E.Start( parser, argv = argv, add_output_options = True )

    ##################################################
    description_header, descriptions, description_width = IO.readDescriptions( options )

    ##################################################
    size_pos, size_segment = GatSegmentList.getSegmentSize()
    E.debug( "sizes: pos=%i segment=%i, max_coord=%i" % (size_pos, size_segment, 2**(8 * size_pos )))

    ##################################################
    # set default counter
    if not options.counters:
        options.counters.append( "nucleotide-overlap" )

    ##################################################
    if options.output_tables_pattern != None: 
        if "%s" not in options.output_tables_pattern:
            raise ValueError( "output_tables_pattern should contain at least one '%s'")

    if options.output_samples_pattern != None: 
        if "%s" not in options.output_samples_pattern:
            raise ValueError( "output_samples_pattern should contain at least one '%s'")

    if options.output_counts_pattern != None: 
        if "%s" not in options.output_counts_pattern:
            raise ValueError( "output_counts_pattern should contain at least one '%s'")


    ##################################################
    # read fold changes that results should be compared with
    if options.null != "default":
        if not os.path.exists( options.null ):
            raise OSError( "file %s not found" % options.null )
        E.info( "reading reference results from %s" % options.null )
        options.reference = IO.readAnnotatorResults( options.null )
    else:
        options.reference = None

    if options.input_filename_counts:
        # use pre-computed counts
        annotator_results = GatEngine.fromCounts( options.input_filename_counts )

    elif options.input_filename_results:
        # use previous results (re-computes fdr)
        E.info( "reading gat results from %s" % options.input_filename_results )
        annotator_results = IO.readAnnotatorResults( options.input_filename_results )

    else:
        # do full gat analysis
        annotator_results = fromSegments( options, args )

    ##################################################
    if options.pvalue_method != "empirical":
        E.info("updating pvalues to %s" % options.pvalue_method )
        GatEngine.updatePValues( annotator_results, options.pvalue_method )

    ##################################################
    ## output
    IO.outputResults( annotator_results, 
                      options, 
                      GatEngine.AnnotatorResultExtended.headers,
                      description_header, 
                      description_width,
                      descriptions )

    IO.plotResults( annotator_results, options )

    ## write footer and output benchmark information.
    E.Stop()

if __name__ == "__main__":
    sys.exit( main( sys.argv) )