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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2014 Daniel Standage <daniel.standage@gmail.com>
# Copyright (c) 2008-2009 Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
# Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#
from ctypes import CFUNCTYPE, c_char_p, c_void_p
from gt.dlload import gtlib, CollectFunc
from gt.core.error import Error, gterror
from gt.core.gtstr import Str
from gt.core.str_array import StrArray
from gt.extended.genome_node import GenomeNode
from gt.props import cachedproperty
AttrIterFunc = CFUNCTYPE(c_char_p, c_char_p, c_void_p)
class FeatureNode(GenomeNode):
def __init__(self):
self.depth_first = True
pass
@classmethod
def create_new(cls, seqid, type, start, end, strand):
from gt.extended.strand import strandchars
if not strand in strandchars:
gterror("Invalid strand '%s' -- must be one of %s" % (strand,
strandchars))
s = Str(seqid.encode("utf-8"))
fn = gtlib.gt_feature_node_new(s._as_parameter_,
type.encode('UTF-8'), start, end,
strandchars.index(str(strand)))
n = cls.create_from_ptr(fn, True)
n.depth_first = True
return n
def update_attrs(self):
attribs = {}
def py_collect_func(tag, val, data):
attribs[tag.decode('UTF-8')] = val.decode('UTF-8')
collect_func = CollectFunc(py_collect_func)
gtlib.gt_feature_node_foreach_attribute(self.gn, collect_func, None)
return attribs
def add_child(self, node):
ownid = str(self.get_seqid())
newid = str(node.get_seqid())
if (ownid != newid):
gterror("cannot add node with sequence region '%s' to node with sequence region '%s'" % (
ownid, newid))
else:
gtlib.gt_feature_node_add_child(self.gn, node._as_parameter_)
def from_param(cls, obj):
if not isinstance(obj, FeatureNode):
raise TypeError("argument must be a FeatureNode")
return obj._as_parameter_
from_param = classmethod(from_param)
def get_source(self):
return gtlib.gt_feature_node_get_source(self.gn)
def set_source(self, source):
s = Str(str(source.encode("utf-8")))
gtlib.gt_feature_node_set_source(self.gn, s._as_parameter_)
source = cachedproperty(get_source, set_source)
def get_type(self):
return gtlib.gt_feature_node_get_type(self.gn).decode('UTF-8')
def set_type(self, type):
gtlib.gt_feature_node_set_type(self.gn, type.encode('UTF-8'))
type = cachedproperty(get_type, set_type)
def has_type(self, type):
return gtlib.gt_feature_node_has_type(self.gn,
type.encode('UTF-8')) == 1
def set_strand(self, strand):
from gt.extended.strand import strandchars
if not strand in strandchars:
gterror("Invalid strand '%s' -- must be one of %s" % (strand,
strandchars))
gtlib.gt_feature_node_set_strand(self.gn, strandchars.index(strand))
def get_strand(self):
from gt.extended.strand import strandchars
return strandchars[gtlib.gt_feature_node_get_strand(self.gn)]
strand = cachedproperty(get_strand, set_strand)
def get_phase(self):
return gtlib.gt_feature_node_get_phase(self.gn)
def set_phase(self, phase):
return gtlib.gt_feature_node_set_phase(self.gn, phase)
phase = cachedproperty(get_phase, set_phase)
def score_is_defined(self):
return gtlib.gt_feature_node_score_is_defined(self.gn) == 1
def get_score(self):
if gtlib.gt_feature_node_score_is_defined(self.gn) == 1:
return gtlib.gt_feature_node_get_score(self.gn)
else:
return None
def set_score(self, score):
gtlib.gt_feature_node_set_score(self.gn, score)
def unset_score(self):
gtlib.gt_feature_node_unset_score(self.gn)
score = cachedproperty(get_score, set_score, unset_score)
def get_attribute(self, attrib):
val = gtlib.gt_feature_node_get_attribute(self.gn,
str(attrib).encode("UTF-8"))
if val == None:
return None
else:
return val.decode("UTF-8")
def add_attribute(self, attrib, value):
if attrib == "" or value == "":
gterror("attribute keys or values must not be empty!")
gtlib.gt_feature_node_add_attribute(self.gn,
str(attrib).encode("UTF-8"),
str(value).encode("UTF-8"))
def each_attribute(self):
attribs = self.update_attrs()
for (tag, val) in list(attribs.items()):
yield (tag, val)
def get_attribs(self):
return dict(self.each_attribute())
attribs = property(get_attribs)
def register(cls, gtlib):
from ctypes import c_char_p, c_float, c_int, c_int, c_void_p, \
c_ulong, c_float
gtlib.gt_feature_node_add_attribute.restype = None
gtlib.gt_feature_node_add_attribute.argtypes = [c_void_p, c_char_p,
c_char_p]
gtlib.gt_feature_node_add_child.restype = None
gtlib.gt_feature_node_add_child.argtypes = [c_void_p,
c_void_p]
gtlib.gt_feature_node_foreach_attribute.restype = None
gtlib.gt_feature_node_foreach_attribute.argtypes = [c_void_p,
c_void_p, c_void_p]
gtlib.gt_feature_node_get_attribute.restype = c_char_p
gtlib.gt_feature_node_get_attribute.argtypes = [c_void_p,
c_char_p]
gtlib.gt_feature_node_get_phase.restype = c_int
gtlib.gt_feature_node_get_phase.argtypes = [c_void_p]
gtlib.gt_feature_node_get_score.restype = c_float
gtlib.gt_feature_node_get_score.argtypes = [c_void_p]
gtlib.gt_feature_node_get_source.restype = c_char_p
gtlib.gt_feature_node_get_source.argtypes = [c_void_p]
gtlib.gt_feature_node_get_strand.restype = c_int
gtlib.gt_feature_node_get_strand.argtypes = [c_void_p]
gtlib.gt_feature_node_get_type.restype = c_char_p
gtlib.gt_feature_node_get_type.argtypes = [c_void_p]
gtlib.gt_feature_node_has_type.restype = c_int
gtlib.gt_feature_node_has_type.argtypes = [c_void_p, c_char_p]
gtlib.gt_feature_node_new.restype = c_void_p
gtlib.gt_feature_node_new.argtypes = [c_void_p, c_char_p, c_ulong,
c_ulong, c_int]
gtlib.gt_feature_node_score_is_defined.restype = c_int
gtlib.gt_feature_node_score_is_defined.argtypes = [c_void_p]
gtlib.gt_feature_node_set_phase.restype = None
gtlib.gt_feature_node_set_phase.argtypes = [c_void_p, c_int]
gtlib.gt_feature_node_set_score.restype = None
gtlib.gt_feature_node_set_score.argtypes = [c_void_p, c_float]
gtlib.gt_feature_node_set_source.restype = None
gtlib.gt_feature_node_set_source.argtypes = [c_void_p, c_void_p]
gtlib.gt_feature_node_set_strand.restype = None
gtlib.gt_feature_node_set_strand.argtypes = [c_void_p, c_int]
gtlib.gt_feature_node_set_type.restype = None
gtlib.gt_feature_node_set_type.argtypes = [c_void_p, c_char_p]
gtlib.gt_feature_node_unset_score.restype = None
gtlib.gt_feature_node_unset_score.argtypes = [c_void_p]
register = classmethod(register)
def traverse(self, it):
f = it.next()
while f is not None:
yield f
f = it.next()
def __iter__(self):
if self.depth_first:
it = FeatureNodeIteratorDepthFirst(self)
else:
it = FeatureNodeIteratorDirect(self)
return self.traverse(it)
def __call__(self, method=None):
if str(method).lower() == 'direct':
it = FeatureNodeIteratorDirect(self)
else:
it = FeatureNodeIteratorDepthFirst(self)
return self.traverse(it)
def traverse_dfs(self):
it = FeatureNodeIteratorDepthFirst(self)
return self.traverse(it)
def traverse_direct(self):
it = FeatureNodeIteratorDirect(self)
return self.traverse(it)
class FeatureNodeIterator(object):
def next(self):
ret = gtlib.gt_feature_node_iterator_next(self.i)
if ret != None:
return FeatureNode.create_from_ptr(ret)
return ret
def __del__(self):
try:
gtlib.gt_feature_node_iterator_delete(self.i)
except AttributeError:
pass
def register(cls, gtlib):
from ctypes import c_void_p
gtlib.gt_feature_node_iterator_delete.restype = c_void_p
gtlib.gt_feature_node_iterator_delete.argtypes = [c_void_p]
gtlib.gt_feature_node_iterator_new.restype = c_void_p
gtlib.gt_feature_node_iterator_new.argtypes = [c_void_p]
gtlib.gt_feature_node_iterator_new_direct.restype = c_void_p
gtlib.gt_feature_node_iterator_new_direct.argtypes = [c_void_p]
gtlib.gt_feature_node_iterator_next.restype = c_void_p
gtlib.gt_feature_node_iterator_next.argtypes = [c_void_p]
register = classmethod(register)
class FeatureNodeIteratorDepthFirst(FeatureNodeIterator):
"""
includes the node itself
"""
def __init__(self, node):
self.i = gtlib.gt_feature_node_iterator_new(node._as_parameter_)
self._as_parameter_ = self.i
class FeatureNodeIteratorDirect(FeatureNodeIterator):
def __init__(self, node):
self.i = gtlib.gt_feature_node_iterator_new_direct(node._as_parameter_)
self._as_parameter_ = self.i
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