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 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 encode(self, seqfiles, indexname):
if not isinstance(seqfiles, list):
raise TypeError, "argument must be a list of strings"
if len(seqfiles) == 0:
raise Error, "list of input sequence files must be non-empty"
sa = StrArray()
for f in seqfiles:
if not os.path.exists(str(f)):
raise IOError, ("file not found: %s" % str(f))
sa.add(str(f))
err = Error()
esptr = gtlib.gt_encseq_encoder_encode(self.ee, sa, str(indexname), err)
if esptr != 0:
gterror(err)
def create_from_sequence(seqfilenames):
if not isinstance(seqfilenames, list):
raise TypeError, "argument must be a list of strings"
e = Error()
sa = StrArray()
for f in seqfilenames:
if not os.path.exists(f):
raise IOError, ("file not found: %s" % f)
sa.add(str(f))
a_ptr = gtlib.gt_alphabet_new_from_sequence(sa, e)
a = Alphabet(a_ptr, True)
if a == None:
gterror(e)
else:
return a
def create_from_sequence(seqfilenames):
if not isinstance(seqfilenames, list):
raise TypeError, "argument must be a list of strings"
e = Error()
sa = StrArray()
for f in seqfilenames:
if not os.path.exists(f):
raise IOError, ("file not found: %s" % f)
sa.add(str(f))
a_ptr = gtlib.gt_alphabet_new_from_sequence(sa, e)
a = Alphabet(a_ptr, True)
if a == None:
gterror(e)
else:
return a
def get_seqids(self):
result = []
stra = StrArray(gtlib.gt_feature_index_get_seqids(self.fi))
for i in range(stra.size()):
result.append(stra.get(i))
return result
def get_used_types(self):
str_array_ptr = gtlib.gt_gff3_in_stream_get_used_types(self.gs)
used_types = StrArray(str_array_ptr)
return used_types.to_list()
def filenames(self, num):
arr = StrArray(gtlib.gt_encseq_filenames(seld.encseq))
return arr.to_list()
def get_used_types(self):
str_array_ptr = gtlib.gt_gff3_in_stream_get_used_types(self.gs)
used_types = StrArray(str_array_ptr)
return used_types.to_list()
def filenames(self, num):
arr = StrArray(gtlib.gt_encseq_filenames(seld.encseq))
return arr.to_list()
