def setUp(self):
self.paths = Paths(base_path=self.test_folder)
self.folder_names = [
self.paths.input_folder,
self.paths.output_folder,
self.paths.align_report_folder,
self.paths.raw_stat_data_folder,
self.paths.read_fasta_folder,
self.paths.ref_seq_folder,
self.paths.annotation_folder,
self.paths.read_alignment_index_folder,
self.paths.read_alignments_folder,
self.paths.processed_reads_folder,
self.paths.unaligned_reads_folder,
self.paths.coverage_raw_folder,
self.paths.coverage_tnoar_min_norm_folder,
self.paths.coverage_tnoar_mil_norm_folder,
self.paths.gene_quanti_base_folder,
self.paths.gene_wise_quanti_combined_path,
]
self.static_files = [
self.paths.read_processing_stats_path,
self.paths.read_alignments_stats_path,
self.paths.read_file_stats,
self.paths.read_alignment_stats_table_path,
self.paths.ref_seq_file_stats,
self.paths.index_path,
]
def data_paths():
parser = argparse.ArgumentParser()
parser.add_argument("project_path", default="/tmp/test", nargs="?")
args = parser.parse_args()
args.project_path = "/tmp/test"
paths = Paths(args)
test_folder = "/tmp/test"
test_files = ["foo.fa", "bar.fa"]
test_lib_names = ["foo", "bar"]
folder_names = [
paths.input_folder, paths.output_folder, paths.align_report_folder,
paths.raw_stat_data_folder, paths.read_fasta_folder,
paths.ref_seq_folder, paths.annotation_folder,
paths.read_alignment_index_folder, paths.read_alignments_folder,
paths.processed_reads_folder, paths.unaligned_reads_folder,
paths.coverage_raw_folder, paths.coverage_tnoar_min_norm_folder,
paths.coverage_tnoar_mil_norm_folder, paths.gene_quanti_base_folder,
paths.gene_wise_quanti_combined_path
]
static_files = [
paths.read_processing_stats_path, paths.read_alignments_stats_path,
paths.read_file_stats, paths.read_alignment_stats_table_path,
paths.ref_seq_file_stats, paths.index_path
]
global base_path
global test_folder
global test_files
global test_lib_names
global paths
global folder_names
global static_files
def __init__(self, args):
"""Create an instance."""
self._args = args
self._paths = Paths(args)
self._helpers = Helpers(args)
self._read_files = None
self._ref_seq_files = None
self._align_viz = AlignViz()
def __init__(self, args):
"""Create an instance."""
self._args = args
self._paths = Paths(args.project_path)
self._read_files = None
self._ref_seq_files = None
def __init__(self, args):
self._paths = Paths(args)
self._args = args
def __init__(self, args):
self._args = args
self._paths = Paths(args)
self._helpers = Helpers(args)
def __init__(self, args):
"""Create an instance."""
self._args = args
self._paths = Paths(args)
self._helpers = Helpers(args)
