如何用Python解析层级keg数据并格式化为TSV文件

我有一份带层级信息和KO编号的keg格式数据集，想用Python转换成TSV文件。要求：

• TSV第一列是KO编号，第二列是描述信息，第三列是基于最近'A'段的层级结构，需包含'A'、'B'、'C'开头的元素直到最近的'C'段；
• 同一KO编号对应不同层级时，用'|'在同一行分隔。

下面是输入数据、预期输出和我写的代码，求指导怎么正确实现需求。

输入数据 #

A09100 Metabolism
B
B  09101 Carbohydrate metabolism
C    00010 Glycolysis / Gluconeogenesis [PATH:ko00010]
D      K00844  HK; hexokinase [EC:2.7.1.1]
D      K12407  GCK; glucokinase [EC:2.7.1.2]
D      K00001  E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
B  09103 Lipid metabolism
C    00071 Fatty acid degradation [PATH:ko00071]
D      K00001  E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
A09120 Genetic Information Processing
B
B  09121 Transcription
C    03020 RNA polymerase [PATH:ko03020]
D      K03043  rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]
D      K13797  rpoBC; DNA-directed RNA polymerase subunit beta-beta' [EC:2.7.7.6]

预期输出 #

KO	metadata_KEGG_Description	metadata_KEGG_Pathways
K00844	HK; hexokinase [EC:2.7.1.1]	Metabolism, Carbohydrate metabolism, Glycolysis / Gluconeogenesis
K12407	GCK; glucokinase [EC:2.7.1.2]	Metabolism, Carbohydrate metabolism, Glycolysis / Gluconeogenesis
K00001	E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]	Metabolism, Carbohydrate metabolism, Glycolysis / Gluconeogenesis|Metabolism, Lipid metabolism, Fatty acid degradation
K03043	rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]	Genetic Information Processing, Transcription, RNA polymerase
K13797	rpoBC; DNA-directed RNA polymerase subunit beta-beta' [EC:2.7.7.6]	Genetic Information Processing, Transcription, RNA polymerase

我的代码 #

data = """A09100 Metabolism
B
B  09101 Carbohydrate metabolism
C    00010 Glycolysis / Gluconeogenesis [PATH:ko00010]
D      K00844  HK; hexokinase [EC:2.7.1.1]
D      K12407  GCK; glucokinase [EC:2.7.1.2]
D      K00001  E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
B  09103 Lipid metabolism
C    00071 Fatty acid degradation [PATH:ko00071]
D      K00001  E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
A09120 Genetic Information Processing
B
B  09121 Transcription
C    03020 RNA polymerase [PATH:ko03020]
D      K03043  rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]
D      K13797  rpoBC; DNA-directed RNA polymerase subunit beta-beta' [EC:2.7.7.6]"""

lines = data.split('\n')

result = []

ko = None
description = None
hierarchy_names = []

for line in lines:
    parts = line.strip().split()
    if parts:
        if parts[0].startswith('A'):
            # Reset hierarchy for a new 'A' section
            hierarchy_names = [" ".join(parts[1:])]
        elif parts[0] == 'K':
            ko = parts[0]
            description = " ".join(parts[1:])
        elif parts[0] == 'D' and len(parts) >= 3:
            ko = parts[1]
            description = " ".join(parts[2:])
        else:
            hierarchy_names.append(" ".join(parts[1:]))

    if ko and description:
        hierarchy_str = ", ".join(hierarchy_names)
        result.append([ko, description, hierarchy_str])

# Add the header row
result.insert(0, ["KO", "metadata_KEGG_Description", "metadata_KEGG_Pathways"])

# Specify the filename for the TSV file
tsv_filename = "output_data.tsv"

with open(tsv_filename, 'w') as tsv_file:
    for row in result:
        tsv_file.write("\t".join(row) + "\n")

print(f"Data saved to {tsv_filename}")

问题分析与修正方案 #

你的代码存在两个核心问题：

1. 层级维护混乱：会把空的'B'行加入层级列表，且新的B/C层级只会追加不会替换，导致层级字符串冗余错误；
2. 重复KO未合并：同一KO对应多个层级时会生成多条记录，没有按要求用'|'合并。

修正后的代码 #

data = """A09100 Metabolism
B
B  09101 Carbohydrate metabolism
C    00010 Glycolysis / Gluconeogenesis [PATH:ko00010]
D      K00844  HK; hexokinase [EC:2.7.1.1]
D      K12407  GCK; glucokinase [EC:2.7.1.2]
D      K00001  E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
B  09103 Lipid metabolism
C    00071 Fatty acid degradation [PATH:ko00071]
D      K00001  E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
A09120 Genetic Information Processing
B
B  09121 Transcription
C    03020 RNA polymerase [PATH:ko03020]
D      K03043  rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]
D      K13797  rpoBC; DNA-directed RNA polymerase subunit beta-beta' [EC:2.7.7.6]"""

lines = data.split('\n')

# 用字典存储KO的描述和层级集合，自动去重合并
ko_dict = {}
current_a = ""
current_b = ""
current_c = ""

for line in lines:
    line = line.strip()
    if not line:
        continue
    # 只分割第一部分，保留描述中的空格
    parts = line.split(maxsplit=1)
    if len(parts) < 1:
        continue
    
    if parts[0].startswith('A'):
        current_a = parts[1] if len(parts) > 1 else parts[0]
        current_b = ""
        current_c = ""
    elif parts[0] == 'B':
        # 跳过空的B行
        if len(parts) > 1:
            current_b = parts[1]
    elif parts[0] == 'C':
        if len(parts) > 1:
            # 去掉PATH后缀，只保留路径名称
            current_c = parts[1].split(' [PATH')[0]
    elif parts[0] == 'D':
        d_parts = parts[1].split(maxsplit=1)
        if len(d_parts) < 2:
            continue
        ko_id = d_parts[0]
        desc = d_parts[1]
        # 组装完整层级字符串
        hierarchy = ", ".join([current_a, current_b, current_c])
        # 更新字典：已存在则添加层级，不存在则新增
        if ko_id in ko_dict:
            ko_dict[ko_id]['hierarchies'].add(hierarchy)
        else:
            ko_dict[ko_id] = {
                'description': desc,
                'hierarchies': {hierarchy}
            }

# 生成最终结果列表
result = [["KO", "metadata_KEGG_Description", "metadata_KEGG_Pathways"]]
# 按KO编号排序输出
for ko_id in sorted(ko_dict.keys()):
    info = ko_dict[ko_id]
    # 用|分隔多个层级
    hierarchy_str = '|'.join(info['hierarchies'])
    result.append([ko_id, info['description'], hierarchy_str])

# 写入TSV文件，指定编码避免乱码
tsv_filename = "output_data.tsv"
with open(tsv_filename, 'w', encoding='utf-8') as tsv_file:
    for row in result:
        tsv_file.write("\t".join(row) + "\n")

print(f"数据已保存到 {tsv_filename}")

修正说明 #

1. 精准层级维护：单独维护current_a/current_b/current_c变量，跳过空B行，自动去除C行的[PATH:xxx]后缀；
2. 字典去重合并：用字典存储每个KO的信息，层级用集合自动去重，同一KO的多个层级最终用'|'连接；
3. 字符串分割优化：用split(maxsplit=1)确保描述中的空格不被拆分，保留完整描述内容；
4. 编码规范：指定utf-8编码写入文件，避免特殊字符乱码。

内容的提问来源于stack exchange，提问作者Umar