comparison data_manager/data_manager_snpEff_databases.py @ 6:2107b4f40945 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit e32db0704e23d58358f749177988d2cb5f01c708

5:3d9dd4b9fb09

    return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
    if return_code:
        sys.exit( return_code )
    databases_output.close()
    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
    data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] )
    data_table_entries = []
    with open(databases_path, 'r') as fh:
        for i, line in enumerate(fh):
            fields = line.split('\t')
            if len(fields) >= 2:

                # snpeff test genome
                if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
                    continue
                description = fields[1].strip() + ' : ' + genome_version
                data_table_entries.append(dict(value=genome_version, name=description))
        data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries
    return data_manager_dict


def main():
    parser = optparse.OptionParser()

6:2107b4f40945

    return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
    if return_code:
        sys.exit( return_code )
    databases_output.close()
    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
    data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get( 'snpeffv_databases', [] )
    data_table_entries = []
    with open(databases_path, 'r') as fh:
        for i, line in enumerate(fh):
            fields = line.split('\t')
            if len(fields) >= 2:

                # snpeff test genome
                if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
                    continue
                description = fields[1].strip() + ' : ' + genome_version
                data_table_entries.append(dict(value=genome_version, name=description))
    data_manager_dict['data_tables']['snpeffv_databases'] = data_table_entries
    return data_manager_dict


def main():
    parser = optparse.OptionParser()