comparison data_manager/data_manager_snpEff_download.py @ 9:08d7998c3afb draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"

8:d107d20dc6bd

    databases_path = 'databases.out'
    databases_output = open(databases_path, 'w')
    args = ['snpEff', 'databases']
    return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
    if return_code:
        sys.exit( return_code )
    databases_output.close()
    try:
        fh = open(databases_path, 'r')
        for i, line in enumerate(fh):
            fields = line.split('\t')

                if genome_version.startswith("Genome") or genome_version.startswith("-"):
                    continue
                description = fields[1].strip()
                snpDBs[genome_version] = description
    except Exception as e:
        stop_err( 'Error parsing %s %s\n' % (databases_path, str( e )) )
    else:
        fh.close()
    return snpDBs

    stderr_path = 'snpeff.err'
    stderr_fh = open(stderr_path, 'w')
    args = ['snpEff', '-h']
    return_code = subprocess.call(args=args, shell=False, stderr=stderr_fh.fileno())
    if return_code != 255:
        sys.exit( return_code )
    stderr_fh.close()
    fh = open(stderr_path, 'r')
    for line in fh:
        m = re.match(r'^[Ss]npEff version (SnpEff)\s*(\d+\.\d+).*$', line)
        if m:

    # Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory
    data_dir = target_directory
    args = ['snpEff', 'download', '-dataDir', data_dir, '-v', genome_version]
    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

            for fname in files:
                if fname.startswith('snpEffectPredictor'):
                    # if snpEffectPredictor.bin download succeeded
                    name = genome_version + (' : ' + organism if organism else '')
                    data_table_entry = dict(key=key, version=snpeff_version, value=genome_version, name=name, path=data_dir)
                    _add_data_table_entry( data_manager_dict, 'snpeffv_genomedb', data_table_entry )
                else:
                    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', {} )
    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
    data_manager_dict['data_tables'][data_table].append( data_table_entry )
    return data_manager_dict


def main():
    parser = optparse.OptionParser()
    parser.add_option( '-g', '--genome_version', dest='genome_version', action='store', type="string", default=None, help='genome_version' )
    parser.add_option( '-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism name' )
    (options, args) = parser.parse_args()

    filename = args[0]

    params = json.loads( open( filename ).read() )
    target_directory = params[ 'output_data' ][0]['extra_files_path']
    os.mkdir( target_directory )
    data_manager_dict = {}

    # Create SnpEff Reference Data
    for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.genome_version, options.organism).split(',')):
        download_database( data_manager_dict, target_directory, genome_version, organism )

    # save info to json file
    open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )


if __name__ == "__main__":
    main()

9:08d7998c3afb

    databases_path = 'databases.out'
    databases_output = open(databases_path, 'w')
    args = ['snpEff', 'databases']
    return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
    if return_code:
        sys.exit(return_code)
    databases_output.close()
    try:
        fh = open(databases_path, 'r')
        for i, line in enumerate(fh):
            fields = line.split('\t')

                if genome_version.startswith("Genome") or genome_version.startswith("-"):
                    continue
                description = fields[1].strip()
                snpDBs[genome_version] = description
    except Exception as e:
        stop_err('Error parsing %s %s\n' % (databases_path, str(e)))
    else:
        fh.close()
    return snpDBs

    stderr_path = 'snpeff.err'
    stderr_fh = open(stderr_path, 'w')
    args = ['snpEff', '-h']
    return_code = subprocess.call(args=args, shell=False, stderr=stderr_fh.fileno())
    if return_code != 255:
        sys.exit(return_code)
    stderr_fh.close()
    fh = open(stderr_path, 'r')
    for line in fh:
        m = re.match(r'^[Ss]npEff version (SnpEff)\s*(\d+\.\d+).*$', line)
        if m:

    # Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory
    data_dir = target_directory
    args = ['snpEff', 'download', '-dataDir', data_dir, '-v', genome_version]
    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

            for fname in files:
                if fname.startswith('snpEffectPredictor'):
                    # if snpEffectPredictor.bin download succeeded
                    name = genome_version + (' : ' + organism if organism else '')
                    data_table_entry = dict(key=key, version=snpeff_version, value=genome_version, name=name, path=data_dir)
                    _add_data_table_entry(data_manager_dict, 'snpeffv_genomedb', data_table_entry)
                else:
                    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', {})
    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
    data_manager_dict['data_tables'][data_table].append(data_table_entry)
    return data_manager_dict


def main():
    parser = optparse.OptionParser()
    parser.add_option('-g', '--genome_version', dest='genome_version', action='store', type="string", default=None, help='genome_version')
    parser.add_option('-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism name')
    (options, args) = parser.parse_args()

    filename = args[0]

    params = json.loads(open(filename).read())
    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)
    data_manager_dict = {}

    # Create SnpEff Reference Data
    for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.genome_version, options.organism).split(',')):
        download_database(data_manager_dict, target_directory, genome_version, organism)

    # save info to json file
    open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True))


if __name__ == "__main__":
    main()