def get_features_for_seqid(self, seqid):
rval = gtlib.gt_feature_index_get_features_for_seqid(self.fi,
seqid)
if rval:
a = Array(rval, True)
result = []
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result
else:
return None
def feature_node_w(fn_p, err_p):
fn = FeatureNode.create_from_ptr(fn_p)
err = Error(err_p)
try:
try:
self.visit_feature_node(fn)
except AttributeError:
pass
return 0
except GTError, errmsg:
err.set(str(errmsg))
return -1
def feature_node_w(fn_p, err_p):
fn = FeatureNode.create_from_ptr(fn_p)
err = Error(err_p)
try:
try:
self.visit_feature_node(fn)
except AttributeError:
pass
return 0
except GTError, errmsg:
err.set(str(errmsg))
return -1
def get_features_for_range(self, start, end, seqid):
from ctypes import byref
a = Array.create()
err = Error()
rng = Range(start, end)
rval = gtlib.gt_feature_index_get_features_for_range(self.fi, a,
seqid, byref(rng), err)
if rval != 0:
gterror(err)
result = []
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result
def get_features_for_seqid(self, seqid):
err = Error()
result = []
rval = gtlib.gt_feature_index_get_features_for_seqid(
self.fi, seqid.encode('UTF-8'), err)
if rval:
a = Array(rval, True)
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result
else:
gterror(err)
return result
def get_features_for_seqid(self, seqid):
err = Error()
result = []
rval = gtlib.gt_feature_index_get_features_for_seqid(self.fi,
seqid, err._as_parameter_)
if rval:
a = Array(rval, True)
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result
else:
gterror(err)
return result
def get_features_for_range(self, start, end, seqid):
from ctypes import byref
a = Array.create()
err = Error()
rng = Range(start, end)
rval = gtlib.gt_feature_index_get_features_for_range(
self.fi, a, seqid, byref(rng), err)
if rval != 0:
gterror(err)
result = []
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result
def get_genome_feature(self):
#refcount only this FeatureNode!
return FeatureNode.create_from_ptr(gtlib.gt_rec_map_get_genome_feature(self.rm),
True)
def visit_feature_node(self, fn):
new_child = FeatureNode.create_new(fn.get_seqid(), "bar", 100, 1000,
"+")
fn.add_child(new_child)
def get_top_level_feature(self):
f = gtlib.gt_block_get_top_level_feature(self.block)
if f != 0:
return FeatureNode.create_from_ptr(f, True)
else:
return None
def get_top_level_feature(self):
f = gtlib.gt_block_get_top_level_feature(self.block)
if f != 0:
return FeatureNode.create_from_ptr(f, True)
else:
return None
def visit_feature_node(self, fn):
new_child = FeatureNode.create_new(fn.get_seqid(), "bar", 100, 1000, "+")
fn.add_child(new_child)
