Python read_csv_metadata_file Examples

Example #1

File: github_files.py Project: ianfoster/crosscut-metadata

def read_protected_wgs_manifest(manifest_file):
    wgs_cram_files = util.read_csv_metadata_file(manifest_file,
                                                 WGS_MANIFEST_COLS,
                                                 'sample_id')
    logging.info("Read " + str(len(wgs_cram_files)) + " CRAM file(s) from " +
                 manifest_file)
    return wgs_cram_files

Example #2

File: github_files.py Project: ianfoster/crosscut-metadata

def read_protected_rnaseq_manifest(manifest_file):
    rnaseq_cram_files = util.read_csv_metadata_file(manifest_file,
                                                    RNASEQ_MANIFEST_COLS,
                                                    'sample_id')
    logging.info("Read " + str(len(rnaseq_cram_files)) +
                 " CRAM file(s) from " + manifest_file)
    return rnaseq_cram_files

Example #3

File: portal_files.py Project: ssun3/crosscut-metadata

def read_sample_attributes_file(samp_att_file):
    samples = util.read_csv_metadata_file(samp_att_file, SAMPLE_ATT_COLS, 'SAMPID')
    logging.info("Read " + str(len(samples)) + " sample(s) from " + samp_att_file)
    return samples

Example #4

File: portal_files.py Project: ssun3/crosscut-metadata

def read_subject_phenotypes_file(subj_phen_file):
    subjects = util.read_csv_metadata_file(subj_phen_file, SUBJ_PHEN_COLS, 'SUBJID')
    logging.info("Read " + str(len(subjects)) + " subject(s) from " + subj_phen_file)
    return subjects

Example #5

File: github_files.py Project: ianfoster/crosscut-metadata

def read_tissue_id_file(id_file):
    tissue_ids = util.read_csv_metadata_file(id_file, TISSUE_ID_COLS,
                                             'Native form')
    logging.info("Read " + str(len(tissue_ids)) + " tissue id(s) from " +
                 id_file)
    return tissue_ids

Example #6

File: github_files.py Project: ianfoster/crosscut-metadata

def read_sample_id_file(id_file):
    sample_ids = util.read_csv_metadata_file(id_file, SAMPLE_ID_COLS,
                                             'Native form')
    logging.info("Read " + str(len(sample_ids)) + " sample id(s) from " +
                 id_file)
    return sample_ids

Example #7

File: github_files.py Project: ianfoster/crosscut-metadata

def read_subject_id_file(id_file):
    subject_ids = util.read_csv_metadata_file(id_file, SUBJECT_ID_COLS,
                                              'Native form')
    logging.info("Read " + str(len(subject_ids)) + " subject id(s) from " +
                 id_file)
    return subject_ids

Example #8

File: manifest_files.py Project: ianfoster/crosscut-metadata

def read_manifest(manifest_file):
    samples = util.read_csv_metadata_file(manifest_file, MANIFEST_COLS, 'sample_id')
    logging.info("Read " + str(len(samples)) + " sample(s) from " + manifest_file)
    return samples

Example #9

File: github_files.py Project: ssun3/crosscut-metadata

def read_dois_manifest(dois_file):
    dois = util.read_csv_metadata_file(dois_file, DOIS_MANIFEST_COLS,
                                       'sample_id')
    logging.info("Read " + str(len(dois)) + " DOI(s) from " + dois_file)
    return dois

Example #10

File: manifest_files.py Project: ssun3/crosscut-metadata

def read_guid_file(guid_file):
    files = util.read_csv_metadata_file(guid_file, GUID_COLS, 'File_Name')
    logging.info("Read " + str(len(files)) + " file(s) from " + guid_file)
    return files