comparison data_manager/data_manager_snpEff_download.py @ 7:a6400027d849 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329

6:2107b4f40945

    return_code = subprocess.call(args=args, shell=False)
    if return_code:
        sys.exit( return_code )
    # search data_dir/genome_version for files
    regulation_pattern = 'regulation_(.+).bin'
    #  annotation files that are included in SnpEff by a flag
    annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif', 'interactions.bin': '-interaction'}
    genome_path = os.path.join(data_dir, genome_version)
    snpeff_version = getSnpeffVersion()
    key = snpeff_version + '_' + genome_version
    if os.path.isdir(genome_path):
        for root, dirs, files in os.walk(genome_path):

                    m = re.match(regulation_pattern, fname)
                    if m:
                        name = m.groups()[0]
                        data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=name, name=name)
                        _add_data_table_entry( data_manager_dict, 'snpeffv_regulationdb', data_table_entry )
                    elif fname in annotations_dict:
                        value = annotations_dict[fname]
                        name = value.lstrip('-')
                        data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=value, name=name)
                        _add_data_table_entry( data_manager_dict, 'snpeffv_annotations', data_table_entry )
    return data_manager_dict


def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )

7:a6400027d849

    return_code = subprocess.call(args=args, shell=False)
    if return_code:
        sys.exit( return_code )
    # search data_dir/genome_version for files
    regulation_pattern = 'regulation_(.+).bin'
    genome_path = os.path.join(data_dir, genome_version)
    snpeff_version = getSnpeffVersion()
    key = snpeff_version + '_' + genome_version
    if os.path.isdir(genome_path):
        for root, dirs, files in os.walk(genome_path):

                    m = re.match(regulation_pattern, fname)
                    if m:
                        name = m.groups()[0]
                        data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=name, name=name)
                        _add_data_table_entry( data_manager_dict, 'snpeffv_regulationdb', data_table_entry )
    return data_manager_dict


def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )