def tab_loader(inputfn, trackfn, genome, parsecols, expectedrows):
buffersize = int(expectedrows / 100)
# element
seqid_col = [col for (col, name, _, _) in parsecols if name == "seqid"][0]
left_col = [col for (col, name, _, _) in parsecols if name == "left"][0]
right_col = [col for (col, name, _, _) in parsecols if name == "right"][0]
# data(s)
for (col, name, _, typ) in parsecols:
dtype = []
data_cols = []
if name not in ("seqid", "left", "right"):
dtype.append(typ)
data_cols.append(col)
#
title = trackfn.split(".")[0]
track = gtrackcore.empty_track(trackfn, genome, expectedrows, title)
#
track.unseal()
arr = track.add_node_values(name, ",".join(dtype))
with open(inputfn) as rh:
nodes = []
datas = []
for i, fields in enumerate(tab_parser_converter(rh, parsecols,
genome)):
node = (fields[seqid_col], fields[left_col], fields[right_col])
nodes.append(node)
data = tuple([fields[data_col] for data_col in data_cols])
datas.append(data[0] if len(data) == 1 else data)
if ((i + 1) % buffersize) == 0:
track.add_nodes(nodes)
arr.append(datas)
track.flush()
nodes, datas = [], []
if nodes:
track.add_nodes(nodes)
arr.append(datas)
track.flush()
track.seal()
return track
def tab_loader(inputfn, trackfn, genome, parsecols, expectedrows):
buffersize = int(expectedrows / 100)
# element
seqid_col = [col for (col, name, _, _) in parsecols if name == "seqid"][0]
left_col = [col for (col, name, _, _) in parsecols if name == "left"][0]
right_col = [col for (col, name, _, _) in parsecols if name == "right"][0]
# data(s)
for (col, name, _, typ) in parsecols:
dtype = []
data_cols = []
if name not in ("seqid", "left", "right"):
dtype.append(typ)
data_cols.append(col)
#
title = trackfn.split(".")[0]
track = gtrackcore.empty_track(trackfn, genome, expectedrows, title)
#
track.unseal()
arr = track.add_node_values(name, ",".join(dtype))
with open(inputfn) as rh:
nodes = []
datas = []
for i, fields in enumerate(tab_parser_converter(rh, parsecols, genome)):
node = (fields[seqid_col], fields[left_col], fields[right_col])
nodes.append(node)
data = tuple([fields[data_col] for data_col in data_cols])
datas.append(data[0] if len (data) == 1 else data)
if ((i + 1) % buffersize) == 0:
track.add_nodes(nodes)
arr.append(datas)
track.flush()
nodes, datas = [], []
if nodes:
track.add_nodes(nodes)
arr.append(datas)
track.flush()
track.seal()
return track
def get_track(self):
fn = self.get_fn()
track = gtrackcore.empty_track(fn, GENOMES["HG19"])
return track
def get_track(self):
fn = self.get_fn()
track = gtrackcore.empty_track(fn, GENOMES["HG19"])
return track
