def stage_input(self, input_ref, fasta_file_extension):
'''
Stage input based on an input data reference for CheckM
input_ref can be a reference to an Assembly, BinnedContigs, or (not yet implemented) a Genome
This method creates a directory in the scratch area with the set of Fasta files, names
will have the fasta_file_extension parameter tacked on.
ex:
staged_input = stage_input('124/15/1', 'fna')
staged_input
{"input_dir": '...'}
'''
# generate a folder in scratch to hold the input
suffix = str(int(time.time() * 1000))
input_dir = os.path.join(self.scratch, 'bins_' + suffix)
all_seq_fasta = os.path.join(self.scratch, 'all_sequences_' + suffix + '.' + fasta_file_extension)
# 2) based on type, download the files
ws = Workspace(self.ws_url)
input_info = ws.get_object_info3({'objects': [{'ref': input_ref}]})['infos'][0]
# 0 obj_id objid - the numerical id of the object.
# 1 obj_name name - the name of the object.
# 2 type_string type - the type of the object.
# 3 timestamp save_date - the save date of the object.
# 4 obj_ver ver - the version of the object.
# 5 username saved_by - the user that saved or copied the object.
# 6 ws_id wsid - the workspace containing the object.
# 7 ws_name workspace - the workspace containing the object.
# 8 string chsum - the md5 checksum of the object.
# 9 int size - the size of the object in bytes.
# 10 usermeta meta - arbitrary user-supplied metadata about
# the object.
obj_name = input_info[1]
type_name = input_info[2].split('-')[0]
if type_name in ['KBaseGenomeAnnotations.Assembly', 'KBaseGenomes.ContigSet']:
au = AssemblyUtil(self.callback_url)
os.makedirs(input_dir)
filename = os.path.join(input_dir, obj_name + '.' + fasta_file_extension)
au.get_assembly_as_fasta({'ref': input_ref, 'filename': filename})
if not os.path.isfile(filename):
raise ValueError('Error generating fasta file from an Assembly or ContigSet with AssemblyUtil')
pass
elif type_name == 'KBaseMetagenomes.BinnedContigs':
# download the bins as fasta and set the input folder name
au = MetagenomeUtils(self.callback_url)
bin_file_dir = au.binned_contigs_to_file({'input_ref': input_ref, 'save_to_shock': 0})['bin_file_directory']
os.rename(bin_file_dir, input_dir)
self.set_fasta_file_extensions(input_dir, fasta_file_extension)
elif type_name == 'KBaseGenomes.Genome':
raise ValueError('Cannot yet stage fasta file input directory from KBaseGenomes.Genome')
else:
raise ValueError('Cannot stage fasta file input directory from type: ' + type_name)
# create summary fasta file with all bins
self.cat_fasta_files(input_dir, fasta_file_extension, all_seq_fasta)
return {'input_dir': input_dir, 'folder_suffix': suffix, 'all_seq_fasta': all_seq_fasta}
