def importAnnotatorGeneSets( infiles, outfile ):
'''import genesets.'''
PAnnotator.importAnnotator( infiles,
outfile,
regex_id = "(.*).sets.annotator",
table = "annotator_sets",
fdr_method = "annotator",
with_slice = True )
def makeAnnotatorGeneSets( infile, outfile, slice ):
'''compute annotator overlap between sets.
'''
workspaces = ("genomic", "alignable", slice )
track = infile[:-len(".gtf.gz")]
infiles = ANNOTATOR_TRACKS
related = getRelatedTracks( infile, infiles )
if related:
E.info("removing related tracks %s from %s" % \
( related, infile ) )
related = set(related)
infiles = [x for x in TRACKS if x not in related ]
tmpdir = tempfile.mkdtemp( dir = os.getcwd() )
annotations = os.path.join( tmpdir, "annotations")
PAnnotator.buildGeneSetAnnotations( infiles,
annotations,
slice )
segments = PAnnotator.buildAnnotatorSlicedSegments( tmpdir,
outfile,
track,
slice )
if not segments:
E.warn( "no segments for %s - no annotator results" % outfile )
shutil.rmtree( tmpdir )
P.touch( outfile )
return
workspaces, synonyms = PAnnotator.buildAnnotatorWorkSpace( tmpdir,
outfile,
workspaces = workspaces,
gc_control = True )
PAnnotator.runAnnotator( tmpdir,
outfile,
annotations,
segments,
workspaces,
synonyms )
shutil.rmtree( tmpdir )
def buildAnnotatorGCWorkspace( infile, outfile ):
'''compute G+C regions.'''
PAnnotator.buildAnnotatorGCWorkspace( infile, outfile )
def buildAnnotatorGeneSetAnnotations( infiles, outfile, slice ):
PAnnotator.buildGeneSetAnnotations( infiles, outfile, slice )
def buildGenomeGCSegmentation( infile, outfile ):
PAnnotator.buildGenomeGCSegmentation( infile, outfile )
