def get_output_files_for_annotation_and_tags(self, annotation, tags):
'''
Retrieve a set of output files of the given annotation, assigned to
the same number of specified tags. If you have two 'alignment' output
files and they are called *out-a.txt* and *out-b.txt*, you can use this
function like this:
- *tags*: ['a', 'b']
- result: {'a': 'out-a.txt', 'b': 'out-b.txt'}
'''
temp = self.get_output_files_abspath()
return misc.assign_strings(temp[annotation].keys(), tags)
def get_output_files_for_annotation_and_tags(self, annotation, tags):
'''
Retrieve a set of output files of the given annotation, assigned to
the same number of specified tags. If you have two 'alignment' output
files and they are called *out-a.txt* and *out-b.txt*, you can use this
function like this:
- *tags*: ['a', 'b']
- result: {'a': 'out-a.txt', 'b': 'out-b.txt'}
'''
temp = self.get_output_files_abspath()
return misc.assign_strings(temp[annotation].keys(), tags)
def declare_runs(self):
for run_id, input_paths in self.get_run_ids_and_input_files_for_connection('in/reads'):
with self.declare_run(run_id) as run:
run.new_exec_group()
is_paired_end = self.find_upstream_info_for_input_paths(input_paths, 'paired_end')
if is_paired_end:
run.add_output_file('reads', "%s-subsample-R1.fastq.gz" % run_id, input_paths)
run.add_output_file('reads', "%s-subsample-R2.fastq.gz" % run_id, input_paths)
else:
raise StandardError("At the moment, random_sample_fastq only supports paired end in this step config")
# in-R1, in-R2, out-R1, out-R2
if not len(input_paths) == 2:
raise StandardError("At the moment, exactly two input files are required.")
input_files = misc.assign_strings(input_paths, ['R1', 'R2'])
run.add_private_info('in-R1', input_files['R1'])
run.add_private_info('in-R2', input_files['R2'])
