139 lines
No EOL
5.9 KiB
Text
139 lines
No EOL
5.9 KiB
Text
from nupack import *
|
||
import subprocess
|
||
import os
|
||
|
||
# ---------- 独立的辅助函数 ----------
|
||
def get_sequence(Complex, result, skip_errors=True):
|
||
"""
|
||
获取复合物的序列。
|
||
- 若 Complex 为 None，返回字典 {复合物名: 序列}，跳过解析失败的复合物。
|
||
- 若 Complex 为字符串或 Complex 对象，返回该复合物的序列字符串；失败时抛出异常（除非 skip_errors=False 时由调用者处理）。
|
||
"""
|
||
# 统一转换为字符串名称
|
||
if Complex is not None and not isinstance(Complex, str):
|
||
Complex = Complex.name if hasattr(Complex, 'name') else str(Complex)
|
||
|
||
def _get_seq_from_strands(strand_names, comp_name=None):
|
||
"""从链名列表获取拼接后的序列，如果失败则抛出异常"""
|
||
seq_parts = []
|
||
for s in strand_names:
|
||
if not s.isidentifier():
|
||
raise NameError(
|
||
f"复合物 '{comp_name}' 中的链名 '{s}' 不是有效的 Python 标识符，"
|
||
"请检查链的 name 属性是否包含空格或特殊字符。"
|
||
)
|
||
try:
|
||
strand_obj = eval(s)
|
||
if not isinstance(strand_obj, Strand):
|
||
raise TypeError(f"'{s}' 不是 Strand 对象")
|
||
seq_parts.append(str(strand_obj))
|
||
except NameError:
|
||
raise NameError(f"链名 '{s}' 未定义，请确保该变量已创建为 Strand 对象。")
|
||
return ''.join(seq_parts)
|
||
|
||
if Complex is None:
|
||
# 批量模式
|
||
sequences = {}
|
||
for comp in result:
|
||
name = comp.name if hasattr(comp, 'name') else str(comp)
|
||
try:
|
||
# 去除括号，按 '+' 分割
|
||
inp = ''.join([ch for ch in name if ch not in '()'])
|
||
strands = inp.split('+')
|
||
sequences[name] = _get_seq_from_strands(strands, comp_name=name)
|
||
except Exception as e:
|
||
if skip_errors:
|
||
print(f"⚠️ 跳过复合物 '{name}'，原因：{e}")
|
||
else:
|
||
raise # 如果不跳过，则抛出异常
|
||
return sequences
|
||
else:
|
||
# 单复合物模式
|
||
inp = ''.join([ch for ch in Complex if ch not in '()'])
|
||
strands = inp.split('+')
|
||
return _get_seq_from_strands(strands, comp_name=Complex)
|
||
|
||
def get_structure(Complex, result, skip_errors=True):
|
||
"""
|
||
获取复合物的 MFE 结构（已去除 '+'）。
|
||
- 若 Complex 为 None，返回字典 {复合物名: 结构}，跳过 result 中不存在的复合物。
|
||
- 若 Complex 为字符串或 Complex 对象，返回该复合物的结构字符串；失败时抛出异常。
|
||
"""
|
||
if Complex is not None and not isinstance(Complex, str):
|
||
Complex = Complex.name if hasattr(Complex, 'name') else str(Complex)
|
||
|
||
if Complex is None:
|
||
structures = {}
|
||
for comp in result:
|
||
name = comp.name if hasattr(comp, 'name') else str(comp)
|
||
try:
|
||
structure = result[comp].mfe[0].structure
|
||
structures[name] = str(structure).replace('+', '')
|
||
except Exception as e:
|
||
if skip_errors:
|
||
print(f"⚠️ 跳过复合物 '{name}'，获取结构失败：{e}")
|
||
else:
|
||
raise
|
||
return structures
|
||
else:
|
||
structure = result[Complex].mfe[0].structure
|
||
return str(structure).replace('+', '')
|
||
|
||
# ---------- 绘图函数（带错误跳过） ----------
|
||
def danlian(Complex, result, output_folder="/home/zsy"):
|
||
"""
|
||
绘制单个复合物的二级结构图。如果处理过程中出现错误，打印错误信息并返回，不中断程序。
|
||
Complex 可为复合物名称字符串或 Complex 对象。
|
||
"""
|
||
try:
|
||
sequence = get_sequence(Complex, result, skip_errors=False) # 这里不跳过，让异常抛出以便捕获
|
||
best_structure = get_structure(Complex, result, skip_errors=False)
|
||
except Exception as e:
|
||
name = Complex if isinstance(Complex, str) else (Complex.name if hasattr(Complex, 'name') else str(Complex))
|
||
print(f"❌ 处理复合物 '{name}' 时出错：{e}，已跳过绘图")
|
||
return
|
||
|
||
# 获取用于文件名的字符串名称
|
||
if isinstance(Complex, str):
|
||
seq_name = Complex
|
||
else:
|
||
seq_name = Complex.name if hasattr(Complex, 'name') else str(Complex)
|
||
|
||
temp_file_path = os.path.join(output_folder, f"{seq_name}.seq")
|
||
try:
|
||
with open(temp_file_path, "w", newline='\n') as f:
|
||
f.write(f">{seq_name}\n")
|
||
f.write(f"{sequence}\n")
|
||
f.write(f"{best_structure}\n")
|
||
except Exception as e:
|
||
print(f"❌ 写入临时文件失败：{e}")
|
||
return
|
||
|
||
try:
|
||
input_filename = f"{seq_name}.seq"
|
||
process = subprocess.run(["RNAplot", "--o", "svg", input_filename], cwd=output_folder, capture_output=True, text=True)
|
||
if process.returncode == 0:
|
||
print(f"🎉 绘图成功！请前往 {output_folder} 文件夹查看 {seq_name}_ss.svg")
|
||
os.remove(temp_file_path)
|
||
else:
|
||
print(f"❌ RNAplot 运行失败，报错信息：\n{process.stderr}")
|
||
except FileNotFoundError:
|
||
print("❌ 找不到 RNAplot 命令，请确认环境变量。")
|
||
except Exception as e:
|
||
print(f"❌ 绘图过程中出现未知错误：{e}")
|
||
|
||
|
||
使用方法
|
||
算全部结果
|
||
for comp in my_result:
|
||
danlian(comp, my_result, output_folder="/home/zsy")
|
||
|
||
算单个结果
|
||
# 假设您的计算结果保存在 my_result 中
|
||
target = '(Y2+Y3)' # 替换为您的目标复合物名称
|
||
# 输出结构
|
||
print(get_structure(target, my_result))
|
||
# 输出序列
|
||
print(get_sequence(target, my_result))
|
||
# 绘制二级结构图
|
||
danlian(target, my_result, output_folder="/home/zsy") |