def to_str(self):
err = Error()
string = Str()
if gtlib.gt_style_to_str(self.style, string, err) == 0:
return str(string)
else:
gterror(err)
def add_gff3file(self, filename):
err = Error()
rval = gtlib.gt_feature_index_add_gff3file(self.fi,
filename.encode('UTF-8'),
err)
if rval != 0:
gterror(err)
def trackselector(block_ptr, string_ptr, data_ptr):
b = Block(block_ptr)
string = Str(string_ptr)
ret = func(b)
if not ret:
gterror("Track selector callback function must return a string!")
string.append_cstr(ret)
def to_file(self, filename):
err = Error()
rval = gtlib.gt_canvas_cairo_file_to_file(
self.canvas,
str(filename).encode('UTF-8'), err)
if rval != 0:
gterror(err)
def __init__(self):
err = Error()
ads = gtlib.gt_anno_db_gfflike_new()
if ads == None:
gterror(err)
self.ads = ads
self._as_parameter_ = self.ads
def extract_decoded(self, start, end):
if start < 0 or end >= self.total_length():
gterror("invalid coordinates: %d-%d (allowed: %d-%d)" %
(start, end, 0, self.total_length() - 1))
buf = (c_char * (end - start + 1))()
gtlib.gt_encseq_extract_decoded(self.encseq, buf, start, end)
return string_at(buf, end - start + 1)
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 trackselector(block_ptr, string_ptr, data_ptr):
b = Block(block_ptr)
string = Str(string_ptr)
ret = func(b)
if not ret:
gterror("Track selector callback function must return a string!")
string.append_cstr(ret)
def mirror(self):
if self.is_mirrored():
gterror("encoded sequence is already mirrored")
err = Error()
ret = gtlib.gt_encseq_mirror(self.encseq, err.error)
if ret != 0:
gterror(err)
def __init__(self):
try:
self.next
except AttributeError:
gterror("%s does not implement mandatory method 'next'!" \
% self.__class__.__name__)
def next_w(nodepp, err):
error = Error(err)
try:
nextnode = self.next()
if nextnode:
nodepp[0] = nextnode.gn
else:
nodepp[0] = None
return 0
except GTError as errmsg:
error.set(str(errmsg))
return -1
self.next_cb = NextFunc(next_w)
def free_w(ptr):
self.free()
self.free_cb = FreeFunc(free_w)
self.gs = gtlib.gt_script_wrapper_stream_new(self.next_cb,
self.free_cb)
self._as_parameter_ = self.gs
def __init__(self):
try:
self.next
except AttributeError:
gterror("%s does not implement mandatory method 'next'!" %
self.__class__.__name__)
def next_w(nodepp, err):
error = Error(err)
try:
nextnode = self.next()
if nextnode:
nodepp[0] = nextnode.gn
else:
nodepp[0] = None
return 0
except Error:
import sys
errmsg = sys.exc_info()[1]
error.set(str(errmsg))
return -1
self.next_cb = NextFunc(next_w)
def free_w(ptr):
try:
self.free()
except AttributeError:
pass
self.free_cb = FreeFunc(free_w)
self.gs = gtlib.gt_script_wrapper_stream_new(self.next_cb,
self.free_cb)
self._as_parameter_ = self.gs
def __init__(self, filename):
err = Error()
rdb = gtlib.gt_rdb_sqlite_new(filename, err._as_parameter_)
if rdb == None:
gterror(err)
self.rdb = rdb
self._as_parameter_ = self.rdb
def description(self, num):
if not num < self.num_of_sequences():
gterror("invalid sequence number %d" % num)
desclen = c_ulong()
str_addr = gtlib.gt_encseq_description(
self.encseq, byref(desclen), num)
return str(string_at(str_addr, desclen.value).decode('UTF-8'))
def get_height(self):
err = Error()
height = c_ulong()
gtlib.gt_layout_get_height(self.layout, byref(height), err)
if err.is_set():
gterror(err)
return height.value
def load_str(self, string):
err = Error()
strg = Str(str(string.encode("utf-8")))
rval = gtlib.gt_style_load_str(self.style, strg._as_parameter_,
err._as_parameter_)
if rval != 0:
gterror(err)
def get_first_seqid(self):
err = Error()
str = gtlib.gt_feature_index_get_first_seqid(self.fi, err)
if str == None:
if err.is_set():
gterror(err)
return str
def description(self, num):
if not num < self.num_of_sequences():
gterror("invalid sequence number %d" % num)
desclen = c_ulong()
str_addr = gtlib.gt_encseq_description(self.encseq, byref(desclen),
num)
return str(string_at(str_addr, desclen.value))
def __init__(self, diagram, width, style):
err = Error()
self.layout = gtlib.gt_layout_new(diagram._as_parameter_, width,
style._as_parameter_, err._as_parameter_)
if err.is_set():
gterror(err)
self._as_parameter_ = self.layout
def get_first_seqid(self):
err = Error()
str = gtlib.gt_feature_index_get_first_seqid(self.fi, err._as_parameter_)
if str == None:
if err.is_set():
gterror(err)
return str
def __init__(self, filename):
err = Error()
rdb = gtlib.gt_rdb_sqlite_new(filename, err._as_parameter_)
if rdb == None:
gterror(err)
self.rdb = rdb
self._as_parameter_ = self.rdb
def __init__(self):
err = Error()
ads = gtlib.gt_anno_db_gfflike_new()
if ads == None:
gterror(err)
self.ads = ads
self._as_parameter_ = self.ads
def to_str(self):
err = Error()
string = Str()
if gtlib.gt_style_to_str(self.style, string, err) == 0:
return str(string)
else:
gterror(err)
def extract_decoded(self, start, end):
if start < 0 or end >= self.total_length():
gterror("invalid coordinates: %d-%d (allowed: %d-%d)" % (start, end,
0, self.total_length()-1))
buf = (c_char * (end-start+1))()
gtlib.gt_encseq_extract_decoded(self.encseq, buf, start, end)
return string_at(buf, end-start+1)
def mirror(self):
if self.is_mirrored():
gterror("encoded sequence is already mirrored")
err = Error()
ret = gtlib.gt_encseq_mirror(self.encseq, err.error)
if ret != 0:
gterror(err)
def get_height(self):
err = Error()
height = c_ulong()
gtlib.gt_layout_get_height(self.layout, byref(height), err)
if err.is_set():
gterror(err)
return height.value
def load_str(self, string):
err = Error()
strg = Str(str(string.encode("utf-8")))
rval = gtlib.gt_style_load_str(self.style, strg._as_parameter_,
err._as_parameter_)
if rval != 0:
gterror(err)
def get_feature_index(self, rdb):
err = Error()
fi = gtlib.gt_anno_db_schema_get_feature_index(self.ads, rdb._as_parameter_,
err._as_parameter_)
if fi == None:
gterror(err)
return FeatureIndexFromPtr(fi)
def get_feature_index(self, rdb):
err = Error()
fi = gtlib.gt_anno_db_schema_get_feature_index(self.ads,
rdb._as_parameter_,
err._as_parameter_)
if fi == None:
gterror(err)
return FeatureIndexFromPtr(fi)
def __init__(self, diagram, width, style):
err = Error()
self.layout = gtlib.gt_layout_new(diagram._as_parameter_, width,
style._as_parameter_,
err._as_parameter_)
if err.is_set():
gterror(err)
self._as_parameter_ = self.layout
def __init__(self, style, width, height, ii=None):
err = Error()
canvas = gtlib.gt_canvas_cairo_file_new(style, GRAPHICS_PNG, width,
height, ii, err)
if canvas == None:
gterror(err)
self.canvas = canvas
self._as_parameter_ = self.canvas
def to_str(self):
err = Error()
string = Str()
if gtlib.gt_style_to_str(self.style, string._as_parameter_,
err._as_parameter_) == 0:
return str(string)
else:
gterror(err)
def to_file(self, filename):
err = Error()
rval = gtlib.gt_canvas_cairo_file_to_file(self.canvas,
str(filename).encode(
'UTF-8'),
err)
if rval != 0:
gterror(err)
def __init__(self, style, width, height, ii=None):
err = Error()
canvas = gtlib.gt_canvas_cairo_file_new(style, GRAPHICS_PNG, width,
height, ii, err)
if canvas == None:
gterror(err)
self.canvas = canvas
self._as_parameter_ = self.canvas
def to_str(self):
err = Error()
string = Str()
if gtlib.gt_style_to_str(self.style, string._as_parameter_,
err._as_parameter_) == 0:
return str(string)
else:
gterror(err)
def get_range_for_seqid(self, seqid):
from ctypes import byref
if gtlib.gt_feature_index_has_seqid(self.fi, seqid) == 0:
gterror("feature_index does not contain seqid")
range = Range()
gtlib.gt_feature_index_get_range_for_seqid(self.fi, byref(range),
seqid)
return range
def get_first_seqid(self):
err = Error()
str = gtlib.gt_feature_index_get_first_seqid(self.fi,
err._as_parameter_)
if str == None:
if err.is_set():
gterror(err)
return str.decode('UTF-8')
def get_seqids(self):
result = []
err = Error()
stra = StrArray(gtlib.gt_feature_index_get_seqids(self.fi, err))
if stra == None:
gterror(err)
for i in range(stra.size()):
result.append(stra.get(i))
return result
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)
fn = gtlib.gt_feature_node_new(s, type, start, end, strandchars.index(strand))
n = cls.create_from_ptr(fn, True)
return n
def has_seqid(self, seqid):
from ctypes import c_int, byref
val = c_int()
err = Error()
ret = gtlib.gt_feature_index_has_seqid(self.fi, byref(val), seqid, err)
if ret != 0:
gterror(err)
else:
return (val.value > 0)
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 create_reader_with_readmode(self, readmode, startpos):
if readmode < 0 or readmode > 3:
gterror("invalid readmode!")
if startpos < 0 or startpos >= self.total_length():
gterror("invalid startposition: %d (allowed: %d-%d)" %
(startpos, 0, self.total_length() - 1))
er = gtlib.gt_encseq_create_reader_with_readmode(
self.encseq, readmode, startpos)
return EncseqReader(er, True)
def get_seqids(self):
result = []
err = Error()
stra = StrArray(gtlib.gt_feature_index_get_seqids(self.fi, err))
if stra == None:
gterror(err)
for i in range(stra.size()):
result.append(stra.get(i))
return result
def __init__(self, filename):
try:
p = open(filename)
tmp = p.readline()
p.close()
except:
gterror("File " + filename + " not readable!")
self.gs = gtlib.gt_gff3_in_stream_new_sorted(filename)
self._as_parameter_ = self.gs
def __init__(self, filename):
try:
p = open(filename)
tmp = p.readline()
p.close()
except:
gterror("File " + filename + " not readable!")
self.gs = gtlib.gt_gff3_in_stream_new_sorted(filename)
self._as_parameter_ = self.gs
def create_from_file(indexname):
if not os.path.exists(indexname + ".al1"):
raise IOError, ("file not found: %s" % (indexname + ".al1"))
e = Error()
a_ptr = gtlib.gt_alphabet_new_from_file(str(indexname), e)
a = Alphabet(a_ptr, True)
if a == None:
gterror(e)
else:
return a
def has_seqid(self, seqid):
from ctypes import c_int, byref
val = c_int()
err = Error()
ret = gtlib.gt_feature_index_has_seqid(self.fi, byref(val),
seqid.encode('UTF-8'), err._as_parameter_)
if ret != 0:
gterror(err)
else:
return (val.value > 0)
def from_index(feature_index, seqid, rng, style):
from ctypes import byref
err = Error()
if rng.start > rng.end:
gterror("range.start > range.end")
diagram = gtlib.gt_diagram_new(feature_index, seqid, byref(rng),
style, err)
if err.is_set():
gterror(err)
return Diagram(diagram)
def trackorderer(s1, s2, data_ptr):
ret = func(s1, s2)
try:
if ret is None:
raise ValueError
else:
ret = int(ret)
except ValueError:
gterror("Track ordering function must return a number!")
return ret
def create_reader_with_readmode(self, readmode, startpos):
if readmode < 0 or readmode > 3:
gterror("invalid readmode!")
if startpos < 0 or startpos >= self.total_length():
gterror("invalid startposition: %d (allowed: %d-%d)" % (startpos,
0,
self.total_length()-1))
er = gtlib.gt_encseq_create_reader_with_readmode(self.encseq, readmode,
startpos)
return EncseqReader(er, True)
def next_tree(self):
err = Error()
genome_node = c_void_p()
rval = gtlib.gt_node_stream_next(self.gs, byref(genome_node), err)
if rval != 0:
gterror(err)
if genome_node.value == None:
return None
else:
return GenomeNode.create_from_ptr(genome_node.value)
def get_cstr(self, section, key, gn=None):
string = Str()
err = Error()
rval = gtlib.gt_style_get_str(self.style, section, key, string, gn, err)
if rval == STYLE_OK:
return str(string)
elif rval == STYLE_NOT_SET:
return None
elif rval == STYLE_ERROR:
gterror(err)
def trackorderer(s1, s2, data_ptr):
ret = func(s1, s2)
try:
if ret is None:
raise ValueError
else:
ret = int(ret)
except ValueError:
gterror("Track ordering function must return a number!")
return ret
def from_index(feature_index, seqid, rng, style):
from ctypes import byref
err = Error()
if rng.start > rng.end:
gterror("range.start > range.end")
diagram = gtlib.gt_diagram_new(feature_index, seqid, byref(rng), style,
err)
if err.is_set():
gterror(err)
return Diagram(diagram)
def has_seqid(self, seqid):
from ctypes import c_int, byref
val = c_int()
err = Error()
ret = gtlib.gt_feature_index_has_seqid(self.fi, byref(val),
seqid, err)
if ret != 0:
gterror(err)
else:
return (val.value > 0)
def create_from_file(indexname):
if not os.path.exists(indexname + ".al1"):
raise IOError, ("file not found: %s" % (indexname + ".al1"))
e = Error()
a_ptr = gtlib.gt_alphabet_new_from_file(str(indexname), e)
a = Alphabet(a_ptr, True)
if a == None:
gterror(e)
else:
return a
def get_range_for_seqid(self, seqid):
from ctypes import byref
err = Error()
if self.has_seqid(seqid) == 0:
gterror("feature_index does not contain seqid")
range = Range()
rval = gtlib.gt_feature_index_get_range_for_seqid(self.fi, byref(range),
seqid, err)
if rval != 0:
gterror(err)
return range
def has_seqid(self, seqid):
from ctypes import c_int, byref
val = c_int()
err = Error()
ret = gtlib.gt_feature_index_has_seqid(self.fi, byref(val),
seqid.encode('UTF-8'),
err._as_parameter_)
if ret != 0:
gterror(err)
else:
return (val.value > 0)
def __init__(self, ptr=None):
if ptr:
self.style = ptr
self.own = False
else:
e = Error()
self.style = gtlib.gt_style_new(e)
if self.style == 0 or self.style == None:
gterror(e)
self.own = True
self._as_parameter_ = self.style
def get_cstr(self, section, key, gn=None):
string = Str()
err = Error()
rval = gtlib.gt_style_get_str(self.style, section, key, string, gn,
err)
if rval == STYLE_OK:
return str(string)
elif rval == STYLE_NOT_SET:
return None
elif rval == STYLE_ERROR:
gterror(err)
def next_tree(self):
err = Error()
genome_node = c_void_p()
rval = gtlib.gt_node_stream_next(self.gs, byref(genome_node),
err._as_parameter_)
if rval != 0:
gterror(err)
if genome_node.value == None:
return None
else:
return GenomeNode.create_from_ptr(genome_node.value)