def runTest(self):
for num, info in sorted(samples['small_signals'].items()):
# Prepare paths #
orig_bigwig_path = info['bigwig']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_bigwig_path = temporary_path('.bigwig')
# From bigwig to SQL #
try:
track.convert(orig_bigwig_path,
test_sql_path,
assembly='sacCer2')
except MissingExecutableError as err:
sys.stderr.write("skipping: {0} ".format(err.message))
break
else:
self.assertTrue(assert_file_equal(orig_sql_path,
test_sql_path))
# From SQL to bigwig #
try:
track.convert(test_sql_path, test_bigwig_path)
except MissingExecutableError as err:
sys.stderr.write("skipping: {0} ".format(err.message))
break
else:
self.assertTrue(
assert_file_equal(orig_bigwig_path,
test_bigwig_path,
start_a=1,
start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_bigwig_path)
def runTest(self):
for num, info in sorted(samples['small_signals'].items()):
# Prepare paths #
orig_bigwig_path = info['bigwig']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_bigwig_path = temporary_path('.bigwig')
# From bigwig to SQL #
try:
track.convert(orig_bigwig_path, test_sql_path, assembly='sacCer2')
except MissingExecutableError as err:
sys.stderr.write("skipping: {0} ".format(err.message))
break
else:
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to bigwig #
try:
track.convert(test_sql_path, test_bigwig_path)
except MissingExecutableError as err:
sys.stderr.write("skipping: {0} ".format(err.message))
break
else:
self.assertTrue(assert_file_equal(orig_bigwig_path, test_bigwig_path, start_a=1, start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_bigwig_path)
def runTest(self):
for num, info in sorted(samples['small_signals'].items()):
# Prepare paths #
orig_bigwig_path = info['bigwig']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_bigwig_path = temporary_path('.bigwig')
# From bigwig to SQL #
track.convert(orig_bigwig_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to bigwig #
track.convert(test_sql_path, test_bigwig_path)
self.assertTrue(assert_file_equal(orig_bigwig_path, test_bigwig_path, start_a=1, start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_bigwig_path)
def runTest(self):
for num, info in sorted(samples['gtf_tracks'].items()):
if num == 'GenRep': continue
orig_gtf_path = info['gtf']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_gtf_path = temporary_path('.gtf')
# From GTF to SQL #
track.convert(orig_gtf_path, test_sql_path)
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to GTF #
# Use Track() instead. #
track.convert(test_sql_path, test_gtf_path)
self.assertTrue(assert_file_equal(orig_gtf_path, test_gtf_path, start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_gtf_path)
def runTest(self):
for num, info in sorted(samples['small_features'].items()):
# Prepare paths #
orig_bed_path = info['bed']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_bed_path = temporary_path('.bed')
# From BED to SQL #
track.convert(orig_bed_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to BED #
with track.load(test_sql_path) as t: t.roman_to_integer()
track.convert(test_sql_path, test_bed_path)
self.assertTrue(assert_file_equal(orig_bed_path, test_bed_path, start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_bed_path)
def runTest(self):
for num, info in sorted(samples['gtf_tracks'].items()):
if num == 'GenRep': continue
orig_gtf_path = info['gtf']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_gtf_path = temporary_path('.gtf')
# From GTF to SQL #
track.convert(orig_gtf_path, test_sql_path)
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to GTF #
# Use Track() instead. #
track.convert(test_sql_path, test_gtf_path)
self.assertTrue(
assert_file_equal(orig_gtf_path, test_gtf_path, start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_gtf_path)
def runTest(self):
for num, info in sorted(samples["gff_tracks"].items()):
# Prepare paths #
orig_gff_path = info["gff"]
orig_sql_path = info["sql"]
test_sql_path = temporary_path(".sql")
test_gff_path = temporary_path(".gff")
# From GFF to SQL #
track.convert(orig_gff_path, test_sql_path, assembly="sacCer2")
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to GFF #
with track.load(test_sql_path) as t:
t.roman_to_integer()
track.convert(test_sql_path, test_gff_path)
self.assertTrue(assert_file_equal(orig_gff_path, test_gff_path, start_a=1, start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_gff_path)
def runTest(self):
for num, info in sorted(samples['small_signals'].items()):
# Some files cannot be roundtriped #
if num == 3 or num == 7: continue
# Prepare paths #
orig_wig_path = info['wig']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_wig_path = temporary_path('.wig')
# From WIG to SQL #
track.convert(orig_wig_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to WIG #
with track.load(test_sql_path) as t: t.roman_to_integer()
track.convert(test_sql_path, test_wig_path)
self.assertTrue(assert_file_equal(orig_wig_path, test_wig_path, start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_wig_path)
def runTest(self):
for num, info in sorted(samples['small_features'].items()):
# Prepare paths #
orig_bed_path = info['bed']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_bed_path = temporary_path('.bed')
# From BED to SQL #
track.convert(orig_bed_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to BED #
with track.load(test_sql_path) as t:
t.roman_to_integer()
track.convert(test_sql_path, test_bed_path)
self.assertTrue(
assert_file_equal(orig_bed_path, test_bed_path, start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_bed_path)
def runTest(self):
# Prepare paths #
orig_gzip_path = samples['gzip_tracks'][1]['gzip']
orig_sql_path = samples['small_features'][1]['sql']
test_sql_path = temporary_path('.sql')
# From BED to SQL #
track.convert(orig_gzip_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# Clean up #
os.remove(test_sql_path)
def runTest(self):
info = samples['small_signals'][1]
# Prepare paths #
orig_sql_path = info['sql']
orig_sga_path = info['sga']
test_sga_path = temporary_path('.sga')
# From SGA to SQL #
track.convert(orig_sql_path, test_sga_path, assembly='hg19')
self.assertTrue(assert_file_equal(orig_sga_path, test_sga_path))
# Clean up #
os.remove(test_sga_path)
def runTest(self):
for num, info in sorted(samples['sga_tracks'].items()):
# Prepare paths #
orig_sga_path = info['sga']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
# From SGA to SQL #
track.convert(orig_sga_path, test_sql_path, assembly='hg19')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# Clean up #
os.remove(test_sql_path)
def runTest(self):
for num, info in sorted(samples['yeast_features'].items()):
# Prepare paths #
orig_bed_path = info['bed']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
# From BED to SQL #
track.convert(orig_bed_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# Clean up #
os.remove(test_sql_path)
def runTest(self):
for num, info in sorted(samples['yeast_features'].items()):
# Prepare paths #
orig_bed_path = info['bed']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
# From BED to SQL #
track.convert(orig_bed_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# Clean up #
os.remove(test_sql_path)
def runTest(self):
for num, info in sorted(samples['rand_signals'].items()):
# Prepare paths #
orig_wig_path = info['wig']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
# From WIG to SQL #
track.convert(orig_wig_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# Clean up #
os.remove(test_sql_path)
def runTest(self):
for num, info in sorted(samples['small_signals'].items()):
# Prepare paths #
orig_bigwig_path = info['bigwig']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_bigwig_path = temporary_path('.bigwig')
# From bigwig to SQL #
track.convert(orig_bigwig_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to bigwig #
track.convert(test_sql_path, test_bigwig_path)
self.assertTrue(
assert_file_equal(orig_bigwig_path,
test_bigwig_path,
start_a=1,
start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_bigwig_path)
def runTest(self):
for num, info in sorted(samples['rand_signals'].items()):
# Prepare paths #
orig_wig_path = info['wig']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
# From WIG to SQL #
track.convert(orig_wig_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# Clean up #
os.remove(test_sql_path)
def runTest(self):
for num, info in sorted(samples['small_signals'].items()):
# Some files cannot be roundtriped #
if num == 3 or num == 7: continue
# Prepare paths #
orig_wig_path = info['wig']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_wig_path = temporary_path('.wig')
# From WIG to SQL #
track.convert(orig_wig_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to WIG #
with track.load(test_sql_path) as t:
t.roman_to_integer()
track.convert(test_sql_path, test_wig_path)
self.assertTrue(
assert_file_equal(orig_wig_path, test_wig_path, start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_wig_path)
def runTest(self):
for num, info in sorted(samples['gtf_tracks'].items()):
# This one is too large #
if num == 'GenRep': continue
# Prepare paths #
orig_gtf_path = info['gtf']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
# From GTF to SQL #
track.convert(orig_gtf_path, test_sql_path)
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# Clean up #
os.remove(test_sql_path)
def runTest(self):
for num, info in sorted(samples['gff_tracks'].items()):
# Prepare paths #
orig_gff_path = info['gff']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
test_gff_path = temporary_path('.gff')
# From GFF to SQL #
track.convert(orig_gff_path, test_sql_path, assembly='sacCer2')
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# From SQL to GFF #
with track.load(test_sql_path) as t:
t.roman_to_integer()
track.convert(test_sql_path, test_gff_path)
self.assertTrue(
assert_file_equal(orig_gff_path,
test_gff_path,
start_a=1,
start_b=1))
# Clean up #
os.remove(test_sql_path)
os.remove(test_gff_path)
def runTest(self):
for num, info in sorted(samples['gtf_tracks'].items()):
# This one is too large #
if num == 'GenRep': continue
# Prepare paths #
orig_gtf_path = info['gtf']
orig_sql_path = info['sql']
test_sql_path = temporary_path('.sql')
# From GTF to SQL #
track.convert(orig_gtf_path, test_sql_path)
self.assertTrue(assert_file_equal(orig_sql_path, test_sql_path))
# Clean up #
os.remove(test_sql_path)
