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")