阿拉伯芥基因ID转换（BioMart，CLC Genomics Workbench输出）

要实现阿拉伯芥基因ID转换，可以使用BioMart和CLC Genomics Workbench两个工具来进行转换。下面给出使用这两个工具进行转换的示例代码：

1. 使用BioMart进行基因ID转换：

from biomart import BiomartServer

def convert_gene_id_with_biomart(source_gene_id_list, source_genome, target_genome):
    server = BiomartServer("http://www.ensembl.org/biomart")
    database = server.databases['plants_mart']
    dataset = database.datasets['athaliana_eg_gene']
    
    results = []
    
    for gene_id in source_gene_id_list:
        response = dataset.search({
            'filters': {'source': source_genome, 'target': target_genome, 'query': gene_id},
            'attributes': ['ensembl_gene_id']
        })
        
        for result in response.iter_lines():
            result = result.decode('utf-8')
            if result:
                results.append(result.split('\t')[0])
    
    return results

# 示例用法
source_gene_ids = ['AT1G01040', 'AT2G22630', 'AT3G52430']
source_genome = 'TAIR'
target_genome = 'ENSEMBL'

converted_gene_ids = convert_gene_id_with_biomart(source_gene_ids, source_genome, target_genome)
print(converted_gene_ids)

2. 使用CLC Genomics Workbench进行基因ID转换：

from pygenomics import clc_genomics_workbench

def convert_gene_id_with_clc(source_gene_id_list, source_genome, target_genome):
    clc = clc_genomics_workbench.ClcGenomicsWorkbench()
    clc.set_workbench_path('/path/to/CLC_Genomics_Workbench')
    
    converted_gene_ids = []
    
    for gene_id in source_gene_id_list:
        response = clc.execute_tool('ID Mapping', {
            'Input': gene_id,
            'From': source_genome,
            'To': target_genome
        })
        
        result_lines = response.split('\n')
        if len(result_lines) > 1:
            converted_gene_ids.append(result_lines[1].split('\t')[1])
    
    return converted_gene_ids

# 示例用法
source_gene_ids = ['AT1G01040', 'AT2G22630', 'AT3G52430']
source_genome = 'TAIR'
target_genome = 'ENSEMBL'

converted_gene_ids = convert_gene_id_with_clc(source_gene_ids, source_genome, target_genome)
print(converted_gene_ids)

以上代码示例分别使用了BioMart和CLC Genomics Workbench进行阿拉伯芥基因ID转换。你可以根据自己的需求，选择其中一个工具进行使用。请注意，使用CLC Genomics Workbench进行转换需要事先安装并配置好该软件。