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test_genomedata.py
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test_genomedata.py
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#!/usr/bin/env python
from __future__ import division, with_statement
"""
test_genomedata: DESCRIPTION
"""
__version__ = "$Revision: 7603 $"
# Copyright 2010-2012 Michael M. Hoffman <mmh1@uw.edu>
import os
import sys
from tempfile import mkdtemp, mkstemp
import unittest
import warnings
from numpy import array, isnan, logical_and, logical_not, NAN
from path import path
from genomedata import Genome
from genomedata.load_genomedata import load_genomedata
from genomedata._load_data import load_data
from genomedata._close_data import close_data
from genomedata._erase_data import erase_data
test_filename = lambda filename: os.path.join("data", filename)
def seq2str(seq):
return seq.tostring().lower()
def make_temp_dir():
return mkdtemp(prefix="genomedata.test.")
class GenomedataTesterBase(unittest.TestCase):
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
def assertArraysEqual(self, observed, expected):
expected = array(expected, dtype=observed.dtype)
not_equal = (observed != expected)
# Do some special stuff to allow testing equality between NaN's
both_nan = logical_and(isnan(observed), isnan(observed))
if logical_and(not_equal, logical_not(both_nan)).any():
self.fail("%r != %r" % (observed, expected))
def test_interface(self):
with Genome(self.gdfilepath) as genome:
self.assertTrue("chr1" in genome)
self.assertFalse("chrZ" in genome)
chromosome = genome["chr1"]
# Test tracknames are as expected
self.assertEqual(sorted(chromosome.tracknames_continuous),
sorted(self.tracknames))
# Test tracknames are consistent
self.assertEqual(sorted(genome.tracknames_continuous),
sorted(chromosome.tracknames_continuous))
# Test chromosome attributes
self.assertEqual(chromosome.start, 0)
self.assertEqual(chromosome.end, 24950)
# Test sequence inside of data range
self.assertEqual(seq2str(chromosome.seq[0:20]),
"taaccctaaccctaacccta")
# Test sequence outside of data range
warnings.simplefilter("ignore")
self.assertEqual(seq2str(chromosome.seq[30000]), "n")
warnings.resetwarnings()
# Track ordering should be: placental, primate, vertebrate
self.assertEqual(chromosome.tracknames_continuous, self.tracknames)
# Given track ordering, check multi-track data retrieval
self.assertArraysEqual(chromosome[290, 0:3],
[-2.297, -2.327, -2.320])
# test multi-track data retrieval by list
self.assertArraysEqual(chromosome[290, ["placental", "primate",
"vertebrate"]],
chromosome[290, 0:3])
self.assertArraysEqual(chromosome[290, ["placental",
"vertebrate"]],
[-2.297, -2.320])
self.assertArraysEqual(chromosome[290, [0, 2]],
[-2.297, -2.320])
self.assertArraysEqual(chromosome[290, [2, 0]],
[-2.320, -2.297])
self.assertArraysEqual(chromosome[290, array([1, 0])],
[-2.327, -2.297])
# Test filling of unassigned continuous segments
chromosome = genome["chrY"]
# Get first supercontig
for supercontig in chromosome:
break
self.assertArraysEqual(supercontig.continuous[0, 2], NAN)
def test_repr_str(self):
genome = Genome(self.gdfilepath, mode="r")
self.assertEqual(repr(genome), "Genome('%s', **{'mode': 'r'})" %
self.gdfilepath)
chr = genome["chr1"]
if self.mode == "dir":
self.assertEqual(repr(chr),
"<Chromosome 'chr1', file='%s/chr1.genomedata'>" %
self.gdfilepath)
self.assertEqual(str(chr), "chr1")
elif self.mode == "file":
self.assertEqual(repr(chr),
"<Chromosome 'chr1', file='%s'>" %
self.gdfilepath)
self.assertEqual(str(chr), "chr1")
genome.close()
def test_no_context(self):
genome = Genome(self.gdfilepath)
chr1 = genome["chr1"]
tracknames = genome.tracknames_continuous
data = chr1[100:1000] # Used to segfault
chr2 = genome["chrY"]
chr2.close() # Make sure manual close doesn't break it
self.assertTrue(chr1.isopen)
self.assertFalse(chr2.isopen)
genome.close()
self.assertFalse(chr1.isopen)
self.assertRaises(Exception, iter(chr1).next)
def test_open_chromosomes(self):
genome = Genome(self.gdfilepath)
with genome:
chr1 = genome["chr1"]
chr2 = genome["chr1"] # Memoized
self.assertEqual(chr1, chr2)
chr3 = genome["chrY"]
self.assertEqual(len(genome.open_chromosomes), 2)
self.assertEqual(genome.open_chromosomes, {})
def set_gdfilepath(self, filename):
self.gdfilepath = path(filename).expand()
class GenomedataTester(GenomedataTesterBase):
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)
def tearDown(self):
return
if self.mode == "dir":
self.gdfilepath.rmtree()
elif self.mode == "file":
self.gdfilepath.remove()
else:
self.fail("Unrecognized mode: %s" % self.mode)
def test_add_track(self):
new_track_name, new_track_file = self.new_track
# Open new track
genome = Genome(self.gdfilepath, mode="r+")
with genome:
genome.add_track_continuous(new_track_name)
# Load data for new track
load_data(self.gdfilepath, new_track_name,
test_filename(new_track_file), verbose=self.verbose)
# Close data with new track
close_data(self.gdfilepath, verbose=self.verbose)
# Make sure addition was successful
genome = Genome(self.gdfilepath)
with genome:
# Track ordering should now end with dnase
self.assertEqual(genome.tracknames_continuous,
self.tracknames + [new_track_name])
# Given track ordering, check single track data retrieval
self.assertArraysEqual(genome["chr1"][155:168, new_track_name],
[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0])
def test_delete_tracks(self):
# Test ability to delete a track
trackname = "primate"
old_entry = (290, -2.327)
new_entry = (290, NAN)
# Test value before deleting track
warnings.simplefilter("ignore")
with Genome(self.gdfilepath, "r+") as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[old_entry[0], trackname],
old_entry[1])
chromosome._erase_data(trackname)
warnings.resetwarnings()
# Re-close data
close_data(self.gdfilepath, verbose=self.verbose)
# Test value after deleting track
with Genome(self.gdfilepath) as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[old_entry[0], trackname],
old_entry[1])
def test_replace_track(self):
# Test ability to delete and replace a track
old_trackname = "primate"
old_entry = (290, -2.327)
new_trackname = "placental"
new_entry = (290, -2.297)
# Test value before deleting track
with Genome(self.gdfilepath) as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[old_entry[0], old_trackname],
old_entry[1])
# Remove track
erase_data(self.gdfilepath, old_trackname,
verbose=self.verbose)
# Now replace it with the data from a different track
track_index = self.tracknames.index(new_trackname)
datafile = self.trackfiles[track_index]
load_data(self.gdfilepath, new_trackname, datafile,
verbose=self.verbose)
# Re-close data
close_data(self.gdfilepath, verbose=self.verbose)
# Now test that the data matches the new track data
with Genome(self.gdfilepath) as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[new_entry[0], new_trackname],
new_entry[1])
class GenomedataGivenDataTester(GenomedataTesterBase):
"""
test a given Genomedata file
"""
def setUp(self):
GenomedataTesterBase.setUp(self)
self.tracknames = ["placental", "primate", "vertebrate"]
class GenomedataNoDataTester(unittest.TestCase):
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 tearDown(self):
if self.mode == "dir":
self.gdfilepath.rmtree()
elif self.mode == "file":
self.gdfilepath.remove()
else:
self.fail("Unrecognized mode: %s" % self.mode)
def assertArraysEqual(self, observed, expected):
expected = array(expected, dtype=observed.dtype)
not_equal = (observed != expected)
# Do some special stuff to allow testing equality between NaN's
both_nan = logical_and(isnan(observed), isnan(observed))
if logical_and(not_equal, logical_not(both_nan)).any():
self.fail("%r != %r" % (observed, expected))
def test_add_track(self):
new_track_name, new_track_file = self.new_track
# Open new track
genome = Genome(self.gdfilepath, mode="r+")
with genome:
self.assertEqual(genome.num_tracks_continuous, 0)
genome.add_track_continuous(new_track_name)
# Load data for new track
load_data(self.gdfilepath, new_track_name,
test_filename(new_track_file), verbose=self.verbose)
# Close data with new track
close_data(self.gdfilepath, verbose=self.verbose)
# Make sure addition was successful
genome = Genome(self.gdfilepath)
with genome:
# Track ordering should now end with dnase
self.assertEqual(genome.tracknames_continuous, [new_track_name])
# Given track ordering, check single track data retrieval
self.assertArraysEqual(genome["chr1"][305:310, new_track_name],
[-2.65300012, 0.37200001, 0.37200001,
0.37200001, 0.37099999])
def test_genomedata(*args):
pass
def parse_options(args):
from optparse import OptionParser
usage = "%prog [OPTION]..."
version = "%%prog %s" % __version__
parser = OptionParser(usage=usage, version=version)
options, args = parser.parse_args(args)
if not len(args) == 0:
parser.error("incorrect number of arguments")
return options, args
def main(args=sys.argv[1:]):
options, args = parse_options(args)
return test_genomedata(*args)
if __name__ == "__main__":
sys.exit(main())