def load_objects(self, is_bedgraph, verbose=False, test=False):
"""Load files and initialize object.
*Keyword arguments:*
- is_bedgraph -- Whether regions are in bedgraph format (default = False).
- verbose -- Verbose output (default = False).
- test -- Fetch only 10 regions form each BED files for test.
"""
for i, t in enumerate(self.types):
if verbose:
print("Loading file ",
self.files[self.names[i]],
file=sys.stderr)
if t not in ["regions", "genes"] and verbose:
print("Cannot load objects", file=sys.stderr)
if t == "regions":
regions = GenomicRegionSet(self.names[i])
if is_bedgraph:
regions.read_bedgraph(
os.path.abspath(self.files[self.names[i]]))
else:
regions.read_bed(os.path.abspath(
self.files[self.names[i]]))
if test: regions.sequences = regions.sequences[0:11]
self.objectsDict[self.names[i]] = regions
elif t == "genes":
genes = GeneSet(self.names[i])
genes.read(
os.path.abspath(self.files[self.names[i]])
) # Here change the relative path into absolute path
self.objectsDict[self.names[i]] = genes
def load_objects(self, is_bedgraph, verbose=False):
"""Load files and initialize object"""
for i, t in enumerate(self.types):
if verbose:
print("Loading file ",
self.files[self.names[i]],
file=sys.stderr)
if t not in ["regions", "genes"] and verbose:
print("Cannot load objects", file=sys.stderr)
if t == "regions":
regions = GenomicRegionSet(self.names[i])
if is_bedgraph:
regions.read_bedgraph(
os.path.abspath(self.files[self.names[i]]))
else:
regions.read_bed(
os.path.abspath(self.files[self.names[i]])
) # Here change the relative path into absolute path
self.objectsDict[self.names[i]] = regions
elif t == "genes":
genes = GeneSet(self.names[i])
genes.read(
os.path.abspath(self.files[self.names[i]])
) # Here change the relative path into absolute path
self.objectsDict[self.names[i]] = genes
def load_objects(self, is_bedgraph, verbose=False, test=False):
"""Load files and initialize object.
*Keyword arguments:*
- is_bedgraph -- Whether regions are in bedgraph format (default = False).
- verbose -- Verbose output (default = False).
- test -- Fetch only 10 regions form each BED files for test.
"""
for i, t in enumerate(self.types):
if verbose: print("Loading file ", self.files[self.names[i]], file = sys.stderr)
if t not in ["regions", "genes"] and verbose:
print("Cannot load objects", file=sys.stderr)
if t == "regions":
regions = GenomicRegionSet(self.names[i])
if is_bedgraph:
regions.read_bedgraph(os.path.abspath(self.files[self.names[i]]))
else:
if test:
g = GenomicRegionSet(self.names[i])
g.read_bed(os.path.abspath(self.files[self.names[i]]))
regions.sequences = g.sequences[0:11]
else:
regions.read_bed(os.path.abspath(self.files[self.names[i]])) # Here change the relative path into absolute path
self.objectsDict[self.names[i]] = regions
elif t == "genes":
genes = GeneSet(self.names[i])
genes.read(os.path.abspath(self.files[self.names[i]])) # Here change the relative path into absolute path
self.objectsDict[self.names[i]] = genes