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)