def write(dictionary, path, format=None):
"""Write a dictionary to disk, whatever the format is.
:param dictionary: contains the chromosomes and features.
:type dictionary: dict
:param format: is the path to track file to write to.
:type format: string
:param format: is an optional parameter specifying the format of the track to create when it cannot be guessed from the file extension.
:type format: string
:returns: None
::
from track.memory import read, write
genes = read('tracks/rp_genes.gff')
genes['chrX'][1523] = (183, 195, 'bra', 1.9)
write('tracks/modified.bed', genes)
"""
# Guess the format #
if not format: format = os.path.splitext(path)[1][1:]
check_path(path)
# Do the job #
serializer = get_serializer(path, format)
parser = get_parser(dictionary, 'memory')
return parser(serializer)
def write(dictionary, path, format=None):
"""Write a dictionary to disk, whatever the format is.
:param dictionary: contains the chromosomes and features.
:type dictionary: dict
:param format: is the path to track file to write to.
:type format: string
:param format: is an optional parameter specifying the format of the track to create when it cannot be guessed from the file extension.
:type format: string
:returns: None
::
from track.memory import read, write
genes = read('tracks/rp_genes.gff')
genes['chrX'][1523] = (183, 195, 'bra', 1.9)
write('tracks/modified.bed', genes)
"""
# Guess the format #
if not format: format = os.path.splitext(path)[1][1:]
check_path(path)
# Do the job #
serializer = get_serializer(path, format)
parser = get_parser(dictionary, 'memory')
return parser(serializer)
def read(path, format=None):
"""Loads a track from disk, whatever the format is and puts it in an enourmous dictionary. Contrary to most of the algorithms in this package, this method will load everything into the RAM. Be careful when using this method on large tracks.
:param path: is the path to track file to create.
:type path: string
:param format: is an optional parameter specifying the format of the track to create when it cannot be guessed from the file extension.
:type format: string
:returns: a dictionary containing all features of every chromosome contained in a track.
::
from track.memory import read, write
genes = read('tracks/rp_genes.bed')
print genes['chrX'][1523]
"""
# Guess the format #
if not format: format = determine_format(path)
# Do the job #
serializer = get_serializer(None, 'memory')
parser = get_parser(path, format)
return parser(serializer)
def read(path, format=None):
"""Loads a track from disk, whatever the format is and puts it in an enourmous dictionary. Contrary to most of the algorithms in this package, this method will load everything into the RAM. Be careful when using this method on large tracks.
:param path: is the path to track file to create.
:type path: string
:param format: is an optional parameter specifying the format of the track to create when it cannot be guessed from the file extension.
:type format: string
:returns: a dictionary containing all features of every chromosome contained in a track.
::
from track.memory import read, write
genes = read('tracks/rp_genes.bed')
print genes['chrX'][1523]
"""
# Guess the format #
if not format: format = determine_format(path)
# Do the job #
serializer = get_serializer(None, 'memory')
parser = get_parser(path, format)
return parser(serializer)
name_generator = tempfile._RandomNameSequence()
name_generator.rng.seed(0)
# New track #
self.handler.newTrack("Random track generator")
self.handler.defineFields(["start", "end", "name", "score", "strand"])
self.handler.defineChrmeta(dict([(ch, dict([("length", sys.maxint)])) for ch in chromosomes]))
# Lots of features #
for chrom in chromosomes:
start = 0
for feat in range(int(feature_factor + 4 * feature_factor * random.random())):
start = start + (random.randint(0, 100))
end = start + (random.randint(1, 100))
name = name_generator.next()
score = random.gammavariate(1, 0.1) * 1000
strand = map(lambda x: x == 1 and 1 or -1, [random.randint(0, 1)])[0]
self.handler.newFeature(chrom, (start, end, name, score, strand))
import sys
sql_path = sys.argv[1]
serializer = get_serializer(sql_path, "sql")
parser = RandomTrack()
print parser(serializer)
# -----------------------------------#
# This code was written by the BBCF #
# http://bbcf.epfl.ch/ #
# [email protected] #
# -----------------------------------#
self.handler.defineFields(['start', 'end', 'name', 'score', 'strand'])
self.handler.defineChrmeta(
dict([(ch, dict([('length', sys.maxint)])) for ch in chromosomes]))
# Lots of features #
for chrom in chromosomes:
start = 0
for feat in range(
int(feature_factor +
4 * feature_factor * random.random())):
start = start + (random.randint(0, 100))
end = start + (random.randint(1, 100))
name = name_generator.next()
score = random.gammavariate(1, 0.1) * 1000
strand = map(lambda x: x == 1 and 1 or -1,
[random.randint(0, 1)])[0]
self.handler.newFeature(chrom,
(start, end, name, score, strand))
import sys
sql_path = sys.argv[1]
serializer = get_serializer(sql_path, 'sql')
parser = RandomTrack()
print parser(serializer)
#-----------------------------------#
# This code was written by the BBCF #
# http://bbcf.epfl.ch/ #
# [email protected] #
#-----------------------------------#
