def write(self, source, **kw):
if self.chrfile is None:
self.chrfile = tempfile.NamedTemporaryFile(dir='./',delete=False)
for c,v in self.chrmeta.iteritems():
self.chrfile.write("%s %i\n"%(c,v['length']))
self.chrfile.close()
self.chrfile = os.path.abspath(self.chrfile.name)
self.open()
kw['mode'] = 'append'
try:
with track(self.bedgraph,format='bedgraph',chrmeta=self.chrmeta) as f:
f.write(source,**kw)
except:
os.remove(self.chrfile)
os.remove(self.bedgraph)
raise
def write(self, source, **kw):
if self.chrfile is None:
self.chrfile = tempfile.NamedTemporaryFile(dir='./', delete=False)
for c, v in self.chrmeta.iteritems():
self.chrfile.write("%s %i\n" % (c, v['length']))
self.chrfile.close()
self.chrfile = os.path.abspath(self.chrfile.name)
self.open()
kw['mode'] = 'append'
try:
with track(self.bedgraph, format='bedgraph',
chrmeta=self.chrmeta) as f:
f.write(source, **kw)
except:
os.remove(self.chrfile)
os.remove(self.bedgraph)
raise
def read(self, selection=None, fields=None, **kw):
"""
:param selection: list of dict of the type
`[{'chr':'chr1','start':(12,24)},{'chr':'chr3','end':(25,45)},...]`,
where tuples represent ranges.
:param fields: (list of str) list of field names.
"""
self.open()
if not(fields): fields = self.fields
fields = [f for f in self.fields if f in fields]
reg = self._make_selection(selection)
options = []
if reg[0]: options += ["-chrom="+reg[0]]
if reg[1]: options += ["-start="+reg[1]]
if reg[2]: options += ["-end="+reg[2]]
self._run_tool('bigWigToBedGraph', options+[self.path, self.bedgraph])
t = track(self.bedgraph,format='bedGraph',chrmeta=self.chrmeta,info=self.info)
return t.read(selection=selection,fields=fields,**kw)
def read(self, selection=None, fields=None, **kw):
"""
:param selection: list of dict of the type
`[{'chr':'chr1','start':(12,24)},{'chr':'chr3','end':(25,45)},...]`,
where tuples represent ranges.
:param fields: (list of str) list of field names.
"""
self.open()
if not (fields): fields = self.fields
fields = [f for f in self.fields if f in fields]
reg = self._make_selection(selection)
options = []
if reg[0]: options += ["-chrom=" + reg[0]]
if reg[1]: options += ["-start=" + reg[1]]
if reg[2]: options += ["-end=" + reg[2]]
self._run_tool('bigWigToBedGraph',
options + [self.path, self.bedgraph])
t = track(self.bedgraph,
format='bedGraph',
chrmeta=self.chrmeta,
info=self.info)
return t.read(selection=selection, fields=fields, **kw)
