Python Table.merge方法代码示例

# 需要导入模块: from biom import Table [as 别名]
# 或者: from biom.Table import merge [as 别名]
def merge(table1: biom.Table, table2: biom.Table) -> biom.Table:
    table1_sids = set(table1.ids(axis='sample'))
    table2_sids = set(table2.ids(axis='sample'))
    if len(table1_sids & table2_sids) > 0:
        raise ValueError('Some samples are present in both tables: %s' %
                         ', '.join(table1_sids & table2_sids))
    return table1.merge(table2)

# 需要导入模块: from biom import Table [as 别名]
# 或者: from biom.Table import merge [as 别名]
def create_non_rarefied_biom_artifact(analysis, biom_data, rarefied_table):
    """Creates the initial non-rarefied BIOM artifact of the analysis

    Parameters
    ----------
    analysis : dict
        Dictionary with the analysis information
    biom_data : dict
        Dictionary with the biom file information
    rarefied_table : biom.Table
        The rarefied BIOM table

    Returns
    -------
    int
        The id of the new artifact
    """
    # The non rarefied biom artifact is the initial biom table of the analysis.
    # This table does not currently exist anywhere, so we need to actually
    # create the BIOM file. To create this BIOM file we need: (1) the samples
    # and artifacts they come from and (2) whether the samples where
    # renamed or not. (1) is on the database, but we need to inferr (2) from
    # the existing rarefied BIOM table. Fun, fun...

    with TRN:
        # Get the samples included in the BIOM table grouped by artifact id
        # Note that the analysis contains a BIOM table per data type included
        # in it, and the table analysis_sample does not differentiate between
        # datatypes, so we need to check the data type in the artifact table
        sql = """SELECT artifact_id, array_agg(sample_id)
                 FROM qiita.analysis_sample
                    JOIN qiita.artifact USING (artifact_id)
                 WHERE analysis_id = %s AND data_type_id = %s
                 GROUP BY artifact_id"""
        TRN.add(sql, [analysis['analysis_id'], biom_data['data_type_id']])
        samples_by_artifact = TRN.execute_fetchindex()

        # Create an empty BIOM table to be the new master table
        new_table = Table([], [], [])
        ids_map = {}
        for a_id, samples in samples_by_artifact:
            # Get the filepath of the BIOM table from the artifact
            artifact = Artifact(a_id)
            biom_fp = None
            for _, fp, fp_type in artifact.filepaths:
                if fp_type == 'biom':
                    biom_fp = fp
            # Note that we are sure that the biom table exists for sure, so
            # no need to check if biom_fp is undefined
            biom_table = load_table(biom_fp)
            samples = set(samples).intersection(biom_table.ids())
            biom_table.filter(samples, axis='sample', inplace=True)
            # we need to check if the table has samples left before merging
            if biom_table.shape[0] != 0 and biom_table.shape[1] != 0:
                new_table = new_table.merge(biom_table)
                ids_map.update({sid: "%d.%s" % (a_id, sid)
                                for sid in biom_table.ids()})

        # Check if we need to rename the sample ids in the biom table
        new_table_ids = set(new_table.ids())
        if not new_table_ids.issuperset(rarefied_table.ids()):
            # We need to rename the sample ids
            new_table.update_ids(ids_map, 'sample', True, True)

        sql = """INSERT INTO qiita.artifact
                    (generated_timestamp, data_type_id, visibility_id,
                     artifact_type_id, submitted_to_vamps)
            VALUES (%s, %s, %s, %s, %s)
            RETURNING artifact_id"""
        # Magic number 4 -> visibility sandbox
        # Magix number 7 -> biom artifact type
        TRN.add(sql, [analysis['timestamp'], biom_data['data_type_id'],
                      4, 7, False])
        artifact_id = TRN.execute_fetchlast()

        # Associate the artifact with the analysis
        sql = """INSERT INTO qiita.analysis_artifact
                    (analysis_id, artifact_id)
                 VALUES (%s, %s)"""
        TRN.add(sql, [analysis['analysis_id'], artifact_id])
        # Link the artifact with its file
        dd_id, mp = get_mountpoint('BIOM')[0]
        dir_fp = join(get_db_files_base_dir(), mp, str(artifact_id))
        if not exists(dir_fp):
            makedirs(dir_fp)
        new_table_fp = join(dir_fp, "biom_table.biom")
        with biom_open(new_table_fp, 'w') as f:
            new_table.to_hdf5(f, "Generated by Qiita")

        sql = """INSERT INTO qiita.filepath
                    (filepath, filepath_type_id, checksum,
                     checksum_algorithm_id, data_directory_id)
                 VALUES (%s, %s, %s, %s, %s)
                 RETURNING filepath_id"""
        # Magic number 7 -> filepath_type_id = 'biom'
        # Magic number 1 -> the checksum algorithm id
        TRN.add(sql, [basename(new_table_fp), 7,
                      compute_checksum(new_table_fp), 1, dd_id])
        fp_id = TRN.execute_fetchlast()
        sql = """INSERT INTO qiita.artifact_filepath
#.........这里部分代码省略.........