def setUp(self): # Defaults self.verbose = False self.mode = "dir" self.tracks = {"vertebrate": "chr1.phyloP44way.vertebrate.short.wigFix", "placental": "chr1.phyloP44way.placental.short.wigFix", "primate": "chr1.phyloP44way.primate.short.wigFix"} # Track to be added by test_add_track self.new_track = ("dnase", "chr1.wgEncodeDukeDNaseSeqBase" "OverlapSignalK562V2.wig") # Potentially override defaults self.init() # Call to sub-classed method # Create Genomedata collection from test files seqs = ["chr1.short.fa", "chrY.short.fa.gz"] # Placental includes data for chr1 and chrY if self.mode == "dir": gdfilename = make_temp_dir() elif self.mode == "file": tempfile, gdfilename = mkstemp(prefix="genomedata") os.close(tempfile) os.remove(gdfilename) # Allow load_genomedata to create it else: self.fail("Unrecognized mode: %s" % self.mode) self.gdfilepath = path(gdfilename).expand() self.tracknames = sorted(self.tracks.keys()) # Get resource paths instead of filenames seqfiles = [test_filename(file) for file in seqs] trackfiles = [test_filename(self.tracks[trackname]) for trackname in self.tracknames] self.seqfiles = seqfiles self.trackfiles = trackfiles tracktuples = [(trackname, trackfile) for trackname, trackfile in zip(self.tracknames, self.trackfiles)] load_genomedata(self.gdfilepath, tracktuples, seqfiles, verbose=self.verbose, mode=self.mode) if self.mode == "dir": self.chroms = [val.split(".")[0] for val in seqs] for chrom in self.chroms: filename = os.extsep.join([chrom, "genomedata"]) filepath = self.gdfilepath.joinpath(filename) self.assertTrue(filepath.isfile(), "Chromosome file was not found: %s" % filepath) elif self.mode == "file": self.assertTrue(self.gdfilepath.isfile(), "Genomedata archive was not created: %r" % self.gdfilepath) else: self.fail("Unrecognized mode: %s" % self.mode)
def setUp(self): GenomedataTesterBase.setUp(self) # Create Genomedata collection from test files seqs = ["chr1.short.fa", "chrY.short.fa.gz"] # Placental includes data for chr1 and chrY if self.mode == "dir": gdfilename = make_temp_dir() elif self.mode == "file": tempfile, gdfilename = mkstemp(prefix="genomedata", text=True) os.close(tempfile) os.remove(gdfilename) # Allow load_genomedata to create it else: self.fail("Unrecognized mode: %s" % self.mode) self.set_gdfilepath(gdfilename) self.tracknames = sorted(self.tracks.keys()) # Get resource paths instead of filenames seqfiles = [test_filename(file) for file in seqs] trackfiles = [ test_filename(self.tracks[trackname]) for trackname in self.tracknames ] self.seqfiles = seqfiles self.trackfiles = trackfiles tracktuples = [ (trackname, trackfile) for trackname, trackfile in zip(self.tracknames, self.trackfiles) ] load_genomedata(self.gdfilepath, tracktuples, seqfiles, verbose=self.verbose, mode=self.mode) if self.mode == "dir": self.chroms = [val.split(".")[0] for val in seqs] for chrom in self.chroms: filename = os.extsep.join([chrom, "genomedata"]) filepath = self.gdfilepath.joinpath(filename) self.assertTrue(filepath.isfile(), "Chromosome file was not found: %s" % filepath) elif self.mode == "file": self.assertTrue( self.gdfilepath.isfile(), "Genomedata archive was not created: %r" % self.gdfilepath) else: self.fail("Unrecognized mode: %s" % self.mode)
def setUp(self): # Defaults self.verbose = False self.mode = "dir" # Track to be added by test_add_track self.new_track = ("primate", "chr1.phyloP44way.primate.short.wigFix") # Potentially override defaults self.init() # Call to sub-classed method # Create Genomedata collection from test files seqs = ["chr1.short.fa", "chrY.short.fa.gz"] # Placental includes data for chr1 and chrY if self.mode == "dir": gdfilename = make_temp_dir() elif self.mode == "file": tempfile, gdfilename = mkstemp(prefix="genomedata") os.close(tempfile) os.remove(gdfilename) # Allow load_genomedata to create it else: self.fail("Unrecognized mode: %s" % self.mode) self.gdfilepath = Path(gdfilename).expand() # Get resource paths instead of filenames seqfiles = [test_filename(file) for file in seqs] self.seqfiles = seqfiles load_genomedata(self.gdfilepath, None, seqfiles, verbose=self.verbose, mode=self.mode) if self.mode == "dir": self.chroms = [val.split(".")[0] for val in seqs] for chrom in self.chroms: filename = os.extsep.join([chrom, "genomedata"]) filepath = self.gdfilepath.joinpath(filename) self.assertTrue(filepath.isfile(), "Chromosome file was not found: %s" % filepath) elif self.mode == "file": self.assertTrue( self.gdfilepath.isfile(), "Genomedata archive was not created: %r" % self.gdfilepath) else: self.fail("Unrecognized mode: %s" % self.mode)
def setUp(self): GenomedataTesterBase.setUp(self) # Create Genomedata collection from test files seqs = ["chr1.short.fa", "chrY.short.fa.gz"] # Placental includes data for chr1 and chrY if self.mode == "dir": gdfilename = make_temp_dir() elif self.mode == "file": tempfile, gdfilename = mkstemp(prefix="genomedata") os.close(tempfile) os.remove(gdfilename) # Allow load_genomedata to create it else: self.fail("Unrecognized mode: %s" % self.mode) self.set_gdfilepath(gdfilename) self.tracknames = sorted(self.tracks.keys()) # Get resource paths instead of filenames seqfiles = [test_filename(file) for file in seqs] trackfiles = [test_filename(self.tracks[trackname]) for trackname in self.tracknames] self.seqfiles = seqfiles self.trackfiles = trackfiles tracktuples = [(trackname, trackfile) for trackname, trackfile in zip(self.tracknames, self.trackfiles)] load_genomedata(self.gdfilepath, tracktuples, seqfiles, verbose=self.verbose, mode=self.mode) if self.mode == "dir": self.chroms = [val.split(".")[0] for val in seqs] for chrom in self.chroms: filename = os.extsep.join([chrom, "genomedata"]) filepath = self.gdfilepath.joinpath(filename) self.assertTrue(filepath.isfile(), "Chromosome file was not found: %s" % filepath) elif self.mode == "file": self.assertTrue(self.gdfilepath.isfile(), "Genomedata archive was not created: %r" % self.gdfilepath) else: self.fail("Unrecognized mode: %s" % self.mode)