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 benchmark_creation(file):
old_path = file['path']
new_path = Path(output_directory + old_path.filename + '.sql')
if os.path.exists(str(new_path)): os.remove(str(new_path))
with Timer() as timer: track.convert(str(old_path), str(new_path))
file['new_path'] = new_path
return timer.total_time
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 benchmark_creation(file):
old_path = file['path']
new_path = Path(output_directory + old_path.filename + '.sql')
if os.path.exists(str(new_path)): os.remove(str(new_path))
with Timer() as timer:
track.convert(str(old_path), str(new_path))
file['new_path'] = new_path
return timer.total_time
def create_tracks():
for collection, conversion_info in sorted(collection_conversion.items()):
for track_name, track_info in sorted(samples[collection].items()):
print Color.ylw + "Creating track '" + track_info['name'] + "'" + Color.end
from_path = track_info[conversion_info['from']]
to_path = track_info[conversion_info['to']]
if os.path.exists(to_path): os.remove(to_path)
track.convert(from_path, to_path, assembly = conversion_info['assembly'])
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):
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['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):
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['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['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['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 tosql(fileinfo, seq_name):
"""
Transform a input file to an sql one.
"""
debug('Tosql', 3)
track.convert(fileinfo.extension and (fileinfo.paths['upload_to'], fileinfo.extension) or fileinfo.paths['upload_to'], fileinfo.paths['store'])
with track.load(fileinfo.paths['store'], 'sql', readonly=False) as t:
t.assembly = seq_name
# debug('tosql : btrack.convert("%s", "%s", chrmeta="%s")' % (fileinfo.paths['upload_to'], fileinfo.paths['store'], seq_name), 3)
# btrack.convert(fileinfo.paths['upload_to'], fileinfo.paths['store'], chrmeta=seq_name)
fileinfo.states['instore'] = True
debug('done', 4)
return fileinfo
def dump(self, track_id, format, *args, **kw):
user = handler.user.get_user_in_session(request)
if not checker.can_download(user.id, track_id):
flash("You haven't the right to export any tracks which is not yours", 'error')
raise redirect('../')
_track = DBSession.query(Track).filter(Track.id == track_id).first()
if format == 'sqlite':
response.content_type = 'application/x-sqlite3'
return open(_track.path).read()
else:
tmp_file = tempfile.NamedTemporaryFile(delete=True)
tmp_file.close()
track.convert(_track.path, (tmp_file.name, format))
response.content_type = 'text/plain'
return open(tmp_file.name).read()
def run(create_sql_files=False):
for format, outcomes in challanges.items():
for outcome, paths in outcomes.items():
for path in paths:
name = os.path.basename(path)
dest = os.path.splitext(path)[0] + '.sql'
if os.path.exists(dest): os.remove(dest)
try:
track.convert(path, dest)
except Exception as err:
message(path, name, 'fail', outcome, str(err)[0:160])
else:
message(path, name, 'pass', outcome)
finally:
if not create_sql_files and os.path.exists(dest): os.remove(dest)
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 run(create_sql_files=False):
for format, outcomes in challanges.items():
for outcome, paths in outcomes.items():
for path in paths:
name = os.path.basename(path)
dest = os.path.splitext(path)[0] + '.sql'
if os.path.exists(dest): os.remove(dest)
try:
track.convert(path, dest)
except Exception as err:
message(path, name, 'fail', outcome, str(err)[0:160])
else:
message(path, name, 'pass', outcome)
finally:
if not create_sql_files and os.path.exists(dest):
os.remove(dest)
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 tosql(fileinfo, seq_name):
"""
Transform a input file to an sql one.
"""
debug('Tosql', 3)
track.convert(
fileinfo.extension and
(fileinfo.paths['upload_to'], fileinfo.extension)
or fileinfo.paths['upload_to'], fileinfo.paths['store'])
with track.load(fileinfo.paths['store'], 'sql', readonly=False) as t:
t.assembly = seq_name
# debug('tosql : btrack.convert("%s", "%s", chrmeta="%s")' % (fileinfo.paths['upload_to'], fileinfo.paths['store'], seq_name), 3)
# btrack.convert(fileinfo.paths['upload_to'], fileinfo.paths['store'], chrmeta=seq_name)
fileinfo.states['instore'] = True
debug('done', 4)
return fileinfo
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['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_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['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_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['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['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 device_add ( self, dev ):
tdir = os.path.expanduser(self._conf['track_dir'])
# Log
prod = dev.get_product()
ser = dev.get_serial()
log('device[%s] added (serial=%s)' % (prod, ser))
self.notify('Device Added', 'Device: %s\nSerial: %s' % (prod, ser))
# Read tracks
history = list(reversed(dev.get_history()))
for h in history:
# Ignore short tracks
if h.summary.distance < self._conf['min_distance']: continue
if h.summary.ride_time < self._conf['min_time']: continue
# Check if already cached?
tm = time.gmtime(h.summary.start)
ts = time.strftime('%Y%m%d%H%M%S', tm)
n = ts + '.track'
p = os.path.join(tdir, n)
if os.path.exists(p): continue
# Log
ts = time.strftime('%F %T', tm)
log('device[%s]: track found %s' % (prod, ts))
self.notify('Track', 'Start: %s' % ts)
# Create directory
if not os.path.exists(tdir):
os.makedirs(tdir)
# Get track data (from device)
t = track.convert(h.merged_segments(True))
t = track.fixup(t, self._conf)
# Save in JSON format
open(p, 'w').write(json.dumps(t))
log('device[%s]: track cached' % (prod))
def runTest(self):
in_path = samples['small_features'][1]['sql']
out_path = temporary_path('.bed')
track.convert(in_path, out_path)
#assert_file_equal(out_path, samples['small_features'][1]['bed'])
os.remove(out_path)
def runTest(self):
in_path = samples['small_features'][1]['sql']
out_path = temporary_path('.bed')
track.convert(in_path, out_path)
#assert_file_equal(out_path, samples['small_features'][1]['bed'])
os.remove(out_path)