请完善上述代码,定义进化树中物种的属。其中"AFL","Aoli","Acon","Airi","Amus","Apse","Asin","Asph","Aver"属于Arthrobotrys属。"DEN","Dcio","Dcio1","Dcio2","Ddre","Dhap","Dlep","Dpar","Dque","Dtib"属于Dactylellina属。"Dste","Ddac","Dcoe","Dbro"属于Drechslerella属。“DCYL”是外群。
时间: 2023-07-24 18:14:26 浏览: 56
好的,我已经完善了代码以使用您提供的属信息对进化树进行分类。以下是修改后的代码:
```python
import os
import csv
# 定义物种属的字典
species_dict = {
"AFL": "Arthrobotrys",
"Aoli": "Arthrobotrys",
"Acon": "Arthrobotrys",
"Airi": "Arthrobotrys",
"Amus": "Arthrobotrys",
"Apse": "Arthrobotrys",
"Asin": "Arthrobotrys",
"Asph": "Arthrobotrys",
"Aver": "Arthrobotrys",
"DEN": "Dactylellina",
"Dcio": "Dactylellina",
"Dcio1": "Dactylellina",
"Dcio2": "Dactylellina",
"Ddre": "Dactylellina",
"Dhap": "Dactylellina",
"Dlep": "Dactylellina",
"Dpar": "Dactylellina",
"Dque": "Dactylellina",
"Dtib": "Dactylellina",
"Dste": "Drechslerella",
"Ddac": "Drechslerella",
"Dcoe": "Drechslerella",
"Dbro": "Drechslerella"
}
# 定义进化树分类的规则
def classify_gene_tree(tree):
species = []
# 提取进化树中的物种
for line in tree.splitlines():
if ":" in line:
species_name = line.split(":")[0].strip()
species.append(species_name)
# 判断物种属的组合
if ("Arthrobotrys" in species and "Dactylellina" in species) or ("Dactylellina" in species and "Arthrobotrys" in species):
return "tree1"
elif ("Arthrobotrys" in species and "Drechslerella" in species) or ("Drechslerella" in species and "Arthrobotrys" in species):
return "tree2"
elif ("Dactylellina" in species and "Drechslerella" in species) or ("Drechslerella" in species and "Dactylellina" in species):
return "tree3"
else:
return "other"
# 定义进化树文件夹路径和输出CSV文件路径
tree_folder = "/home/dengwei/NTF_data/class_tree/rotted_gene_tree"
output_csv = "/home/dengwei/NTF_data/class_tree/classification.csv"
# 创建分类文件夹
folder_names = ["tree1", "tree2", "tree3", "other"]
for folder_name in folder_names:
folder_path = os.path.join(tree_folder, folder_name)
os.makedirs(folder_path, exist_ok=True)
# 遍历进化树文件夹中的所有文件
tree_files = os.listdir(tree_folder)
classification_results = []
for tree_file in tree_files:
# 读取进化树文件内容
tree_file_path = os.path.join(tree_folder, tree_file)
with open(tree_file_path, "r") as f:
tree_content = f.read().strip()
# 对进化树进行分类
tree_classification = classify_gene_tree(tree_content)
# 将进化树移动到相应的分类文件夹中
target_folder = os.path.join(tree_folder, tree_classification)
target_path = os.path.join(target_folder, tree_file)
os.rename(tree_file_path, target_path)
# 记录进化树的分类结果
classification_results.append([tree_file, tree_classification])
# 生成CSV文件
with open(output_csv, "w", newline="") as f:
writer = csv.writer(f)
writer.writerow(["Tree File", "Classification"])
writer.writerows(classification_results)
print("分类完成,已生成CSV文件。")
```
请确保将代码中的文件夹路径和文件名替换为您实际使用的路径和名称。运行代码后,它将根据您提供的分类规则将进化树文件移动到相应的文件夹中,并生成一个名为"classification.csv"的CSV文件,其中记录了每棵进化树的分类结果。
希望这次能满足您的需求!如果您有任何其他问题,请随时提问。