def get_results(self):
if self.file_read_job == None:
return self.results
else:
# self.results=read_internal_alignment(self.alignedfn,)
alignment = Alignment()
alignment.datatype = self.datatype
alignment.read_filepath(self.alignedfn, file_format='FASTA')
self.results = alignment
return self.results
def read_internal_alignment(fn, file_format="FASTA", datatype=None, dirs_to_delete=(), temp_fs=None):
alignment = Alignment()
alignment.datatype = datatype
alignment.read_filepath(fn, file_format=file_format)
if len(alignment) >= 1:
if dirs_to_delete:
assert temp_fs
for d in dirs_to_delete:
time.sleep(1) # TODO: not sure why this is here!
temp_fs.remove_dir(d)
return alignment
else:
raise ValueError("The alignment file has no sequences. SATe quits." % fn)
def read_internal_alignment(fn,
file_format='FASTA',
datatype=None,
dirs_to_delete=(),
temp_fs=None):
alignment = Alignment()
alignment.datatype = datatype
alignment.read_filepath(fn, file_format=file_format)
if len(alignment) >= 1:
if dirs_to_delete:
assert (temp_fs)
for d in dirs_to_delete:
time.sleep(.1) #TODO: not sure why this is here!
temp_fs.remove_dir(d)
return alignment
else:
raise ValueError(
"The alignment file %s has no sequences. PASTA quits." % fn)
