def write_sdrf_table_files(i, output_path):
"""Writes out SDRF table files
:param i: ISA Investigation object
:param output_path: Output path to write SDRFs to
:return: None
"""
tmp = tempfile.mkdtemp()
isatab.write_study_table_files(inv_obj=i, output_dir=tmp)
isatab.write_assay_table_files(inv_obj=i, output_dir=tmp)
for study in i.studies:
for assay in [
x for x in study.assays
if x.technology_type.term.lower() == "dna microarray"]:
sdrf_filename = study.filename[2:-3] + \
assay.filename[2:-3] + "sdrf.txt"
log.debug("Writing {}".format(sdrf_filename))
try:
isatab.merge_study_with_assay_tables(
os.path.join(tmp, study.filename),
os.path.join(tmp, assay.filename),
os.path.join(output_path, sdrf_filename))
except FileNotFoundError:
raise IOError("There was a problem merging intermediate "
"ISA-Tab files into SDRF")
def write_sdrf_table_files(i, output_path):
tmp = tempfile.mkdtemp()
isatab.write_study_table_files(inv_obj=i, output_dir=tmp)
isatab.write_assay_table_files(inv_obj=i, output_dir=tmp)
for study in i.studies:
for assay in [x for x in study.assays if x.technology_type.term.lower() == "dna microarray"]:
sdrf_filename = study.filename[2:-3] + assay.filename[2:-3] + "sdrf.txt"
print("Writing {}".format(sdrf_filename))
try:
isatab.merge_study_with_assay_tables(os.path.join(tmp, study.filename),
os.path.join(tmp, assay.filename),
os.path.join(output_path, sdrf_filename))
except FileNotFoundError:
raise IOError("There was a problem merging intermediate ISA-Tab files into SDRF")