def get_expression_tsv(experiment_md):
"""get path to expression TSV file or None if not valid for this
experiment. Will not include .gz extension or check for existence."""
if experiment_md.challenge_id is Challenge.iso_quant:
return existing_datafile_name(
osp.join(experiment_md.experiment_dir, EXPRESSION_TSV))
else:
return None
def get_rna_fasta(experiment_md):
"""get path to RNA fasta file or None if not valid for this
experiment. Will not include .gz extension or check for existence."""
if experiment_md.challenge_id is Challenge.iso_detect_de_novo:
return existing_datafile_name(
osp.join(experiment_md.experiment_dir, DE_NOVO_RNA_FASTA))
else:
return None
def get_models_gtf(experiment_md):
"""get path to models.gtf file or None if not valid for this experiment.
Will not include .gz extension or check for existence."""
if experiment_md.challenge_id in (Challenge.iso_detect_ref,
Challenge.iso_quant):
return existing_datafile_name(
osp.join(experiment_md.experiment_dir, MODELS_GTF))
else:
return None
def get_read_model_map_tsv(experiment_md):
"""get path to read_model_map.gtf file or None if not valid for this
experiment. Will not include .gz extension or check for existence."""
if experiment_md.challenge_id in (Challenge.iso_detect_ref,
Challenge.iso_detect_de_novo):
return existing_datafile_name(
osp.join(experiment_md.experiment_dir, READ_MODEL_MAP_TSV))
else:
return None
def load(model_map_tsv):
read_model_map = ReadModelMap()
try:
with gopen(existing_datafile_name(model_map_tsv)) as fh:
for pair in _tsv_reader(fh):
read_model_map.add(pair)
if len(read_model_map) == 0:
raise LrgaspException("TSV contains no data")
return read_model_map
except (LrgaspException, FileNotFoundError, csv.Error) as ex:
raise LrgaspException("Parse of reads-to-models TSV failed: {}".format(
model_map_tsv)) from ex