layout/tools/t7.py

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import copy
import os
import time
from collections import defaultdict
from datetime import datetime
import pandas as pd
from deap import base, creator, tools, algorithms
from tools.common import basedir, log
# 定义一个格式化函数
def format_date(date):
return date.strftime('%Y-%m-%d')
def count_barcode_radio(data):
df = pd.DataFrame(data)
ratio_sites = dict()
is_not_balance_list = []
if df.empty:
return ratio_sites, is_not_balance_list
df['barcode'] = df['barcode'].str.slice(0, 16)
barcode_df = pd.DataFrame(df['barcode'].str.split('', expand=True).iloc[:, 1:-1].values,
columns=['T' + str(x) for x in range(16)]).join(df['data_needed'])
total = barcode_df['data_needed'].sum()
for i in range(16):
column = 'T' + str(i)
col_df = barcode_df.groupby(column).agg({'data_needed': 'sum'})
# 去掉N计数
if 'N' in col_df.index:
base_n_size = col_df.loc['N', 'data_needed']
col_df = col_df.drop('N')
else:
base_n_size = 0
col_df['ratio'] = (col_df['data_needed']) / (total - base_n_size)
ratio = col_df['ratio'].to_dict()
ratio_sites[i] = ratio
A, B, C, D, E, F = list(), list(), list(), list(), list(), list()
for decbase in ['A', 'T', 'C', 'G']:
if decbase not in ratio:
ratio[decbase] = 0
if ratio[decbase] >= 0.6:
A.append(decbase)
if 0.2 <= ratio[decbase] < 0.6:
B.append(decbase)
if 0.15 <= ratio[decbase] < 0.2:
C.append(decbase)
if 0.1 <= ratio[decbase] < 0.15:
D.append(decbase)
if 0.08 <= ratio[decbase] < 0.1:
E.append(decbase)
if ratio[decbase] < 0.08:
F.append(decbase)
A_num, B_num, C_num, D_num, E_num, F_num = len(A), len(B), len(C), len(D), len(E), len(F)
if not ((B_num + C_num + D_num == 4) or (F_num == 1 and (A_num + B_num) == 3) or (
E_num == 1 and D_num == 1 and (A_num + B_num + C_num) == 2) or (
E_num == 1 and (A_num + B_num + C_num) == 3)):
is_not_balance_list.append(
'%s位置,算出结果为 %s' % (i, ratio)
)
return ratio_sites, is_not_balance_list
# 定义遗传算法
class Ga:
"""
# 定义遗传算法
"""
def __init__(self, sheets):
self.sheets = sheets
# 定义个体的生成方式
def generate_individual(self):
individual = copy.deepcopy(self.sheets) # 初始解作为个体
return [individual]
# 定义评估函数
@staticmethod
def evaluate(individual):
total_data_needed_sum = 0
xchip = 0
try:
for sheetname, data in individual[0][0].items():
library_data = pd.DataFrame(data)
size = library_data['data_needed'].sum()
# 芯片大小不能超过设定限制
if size > 1700:
return (0, 100000, 100000)
# barcode有重复
if len(library_data['barcode'].values) < len(set(library_data['barcode'].values)):
return (0, 100000, 100000)
# 不平衡文库大于250G 不能添加
if library_data[library_data['is_balance_lib'] == '']['data_needed'].sum() > 250:
return (0, 100000, 100000)
# 碱基不平衡不过不添加,保证前面的数据, 在数据达到1200G的时候开始
ratio_sites, is_not_balance_list = count_barcode_radio(library_data)
if is_not_balance_list:
return (0, 100000, 100000)
if library_data[library_data['classification'].str.lower() == 'nextera']['data_needed'].sum() <= 50:
return (0, 100000, 100000)
# 计算每个sheet的data_needed之和
total_data_needed_sum += library_data['data_needed'].sum()
# 记录包含字母"A"的sheet数量
if any('极致' in value for value in library_data['split']):
xchip += 1
except Exception:
return (0, 100000, 100000)
# 返回一个适应度值目标是最大化总的data_needed之和最小化sheet的数量, 最少的极致芯片
total_data_needed_sum, num_sheets, num_xchip = total_data_needed_sum, len(individual[0]), xchip
return total_data_needed_sum, num_sheets, num_xchip
def run(self):
# 定义遗传算法的参数
pop_size = 50
cxpb = 0.7 # 交叉概率
mutpb = 0.2 # 变异概率
ngen = 100 # 迭代次数
# 初始化遗传算法工具箱
creator.create("FitnessMax", base.Fitness, weights=(1.0, -1.0, -1.0,)) # 三个目标,一个最大化两个最小化
creator.create("Individual", list, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
# 结构初始化器
toolbox.register("individual", tools.initRepeat, creator.Individual, self.generate_individual, n=3)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", self.evaluate)
# 注册遗传算法所需的操作
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", tools.mutUniformInt, low=1, up=100, indpb=0.2)
toolbox.register("select", tools.selTournament, tournsize=3)
# 初始化种群
population = toolbox.population(n=pop_size)
# 运行遗传算法
algorithms.eaMuPlusLambda(population, toolbox, mu=pop_size, lambda_=pop_size * 2, cxpb=cxpb, mutpb=mutpb,
ngen=ngen, stats=None, halloffame=None)
# 输出结果
best_individual = tools.selBest(population, k=1)
print(best_individual)
optimized_sheets = best_individual[0] # 获取最优解
# 将优化后的结果输出
# for i, sheet in enumerate(optimized_sheets):
# sheet.to_excel(f'optimized_sheet_{i + 1}.xlsx', index=False)
return optimized_sheets
class AutoLayout:
"""
自动化派样
"""
def __init__(self, path, librarynum, output=basedir, data_limit=1750):
self.path = path
self.output = output
self.librarynum = int(librarynum)
self.data_limit = data_limit
self.index_assignments = defaultdict(list)
# 芯片数量量大小
self.chip_size = dict()
# 芯片是否极致
self.chip_type = dict()
# 芯片barcode
self.chip_barcode_recode = defaultdict(set)
# 芯片原始数据读取
self.ori_data = self.read_excel()
# 当前锚芯片
self.loc_chip_num = 1
# 芯片客户
self.chip_customer = defaultdict(set)
# 文库
self.chip_classification = defaultdict(set)
self.rule = self.read_rule()
# 甲基化文库不大于200,WGBS文库不大于200G
self.chip_speciallib_size = dict()
# Nextera 文库大小
self.chip_speciallib_nextera_size = dict()
self.logger = log(os.path.basename(f'{path}.txt'))
self.return_log = list()
self.no_assign_data = list()
self.need_cols = self.read_cols()
def read_excel(self):
"""
原始数据处理
:return:
"""
merge = pd.read_excel(self.path, None)
ori_data = dict()
for name, sheet in merge.items():
sheet.fillna('', inplace=True)
ori_data[name] = sheet.to_dict('records')
return ori_data
def add_new_data(self, chipname, library_data, newer=True):
"""
增加新数据到已知芯片上
:param chipname:
:param library_data:
:param newer:
:return:
"""
self.index_assignments[chipname].extend(library_data['data'])
self.chip_barcode_recode[chipname].update({item['barcode'] for item in library_data['data']})
self.chip_customer[chipname].add(library_data['customer'])
self.chip_classification[chipname].add(library_data['classification'])
if newer:
self.chip_size[chipname] = library_data['size']
# if library_data['classification'] in ['扩增子', '不平衡文库', '单细胞文库以及甲基化']:
if library_data['is_balance_lib'] == '':
self.chip_speciallib_size[chipname] = library_data['size']
else:
self.chip_speciallib_size[chipname] = 0
if 'nextera' in library_data['classification'].lower():
self.chip_speciallib_nextera_size[chipname] = library_data['size']
else:
self.chip_speciallib_nextera_size[chipname] = 0
else:
self.chip_size[chipname] += library_data['size']
if library_data['is_balance_lib'] == '':
self.chip_speciallib_size[chipname] += library_data['size']
if 'nextera' in library_data['classification'].lower():
self.chip_speciallib_nextera_size[chipname] += library_data['size']
@staticmethod
def count_barcode_radio(data):
df = pd.DataFrame(data)
ratio_sites = dict()
is_not_balance_list = []
if df.empty:
return ratio_sites, is_not_balance_list
df['barcode'] = df['barcode'].str.slice(0, 16)
barcode_df = pd.DataFrame(df['barcode'].str.split('', expand=True).iloc[:, 1:-1].values,
columns=['T' + str(x) for x in range(16)]).join(df['data_needed'])
total = barcode_df['data_needed'].sum()
for i in range(16):
column = 'T' + str(i)
col_df = barcode_df.groupby(column).agg({'data_needed': 'sum'})
# 去掉N计数
if 'N' in col_df.index:
base_n_size = col_df.loc['N', 'data_needed']
col_df = col_df.drop('N')
else:
base_n_size = 0
col_df['ratio'] = (col_df['data_needed']) / (total - base_n_size)
ratio = col_df['ratio'].to_dict()
ratio_sites[i] = ratio
A, B, C, D, E, F = list(), list(), list(), list(), list(), list()
for decbase in ['A', 'T', 'C', 'G']:
if decbase not in ratio:
ratio[decbase] = 0
if ratio[decbase] >= 0.6:
A.append(decbase)
if 0.2 <= ratio[decbase] < 0.6:
B.append(decbase)
if 0.15 <= ratio[decbase] < 0.2:
C.append(decbase)
if 0.1 <= ratio[decbase] < 0.15:
D.append(decbase)
if 0.08 <= ratio[decbase] < 0.1:
E.append(decbase)
if ratio[decbase] < 0.08:
F.append(decbase)
A_num, B_num, C_num, D_num, E_num, F_num = len(A), len(B), len(C), len(D), len(E), len(F)
if not ((B_num + C_num + D_num == 4) or (F_num == 1 and (A_num + B_num) == 3) or (
E_num == 1 and D_num == 1 and (A_num + B_num + C_num) == 2) or (
E_num == 1 and (A_num + B_num + C_num) == 3)):
is_not_balance_list.append(
'%s位置,算出结果为 %s' % (i, ratio)
)
return ratio_sites, is_not_balance_list
def dec_barcode_radio(self, chipname):
data = self.index_assignments[chipname]
ratio_sites, is_not_balance_list = self.count_barcode_radio(data)
if is_not_balance_list:
desc = '\n'.join(is_not_balance_list)
self.return_log.append(f'芯片{chipname}有碱基不平衡:\n{desc}')
print(f'芯片{chipname}有碱基不平衡:\n{desc}')
@staticmethod
def level(row):
today_date = datetime.now()
# 将时间字符串转换为 datetime 对象
# mytime = datetime.strptime(row['time'], "%Y-%m-%d")
# mytime = row['time'].strftime("%Y-%m-%d")
if 'nextera' in row['classification'].lower():
return 1
if row['拆分方式'] == '极致周期' or '极致' in row['拆分方式']:
return 2
mytime = row['time']
# 判断日期是之前的还是之后的
if mytime < today_date:
return 3
if '加急' in row['priority']:
return 4
if '补测' in row['priority']:
return 5
else:
return 100
@staticmethod
def read_rule():
df = pd.read_excel(os.path.join(basedir, 'rule', 'exclusive_classfication.xlsx'))
newdf = pd.DataFrame()
newdf['c1'] = df['c2']
newdf['c2'] = df['c1']
res = pd.concat([df, newdf])
return res.reset_index()
@staticmethod
def read_cols():
df = pd.read_excel(os.path.join(basedir, 'rule', 'columns.xlsx'))
cols = list(df['cols'].values)
return cols
def use_rule(self, chipname, classfication):
may_classfic = set(self.rule[self.rule['c1'] == classfication]['c2'])
if self.chip_customer[chipname].intersection(may_classfic):
return True
return False
def judge_data(self, chipname, library_data):
size = library_data['size']
# customer = library_data['customer']
# library = library_data['library']
classification = library_data['classification']
is_balance_lib = library_data['is_balance_lib']
# 芯片大小不能超过设定限制
sizelimit = True
if self.chip_size[chipname] + size > self.data_limit:
sizelimit = False
# barcode有重复
notrepeatbarcode = True
if self.chip_barcode_recode[chipname].intersection({item['barcode'] for item in library_data['data']}):
notrepeatbarcode = False
# 互斥的文库
exclusive_classific = True
if self.use_rule(chipname, classification):
exclusive_classific = False
# 不平衡文库大于250G 不能添加
splibrary = True
if is_balance_lib == '' and self.chip_speciallib_size[chipname] + size > 250:
splibrary = False
# 碱基不平衡不过不添加,保证前面的数据, 在数据达到1200G的时候开始
base_balance = True
if self.chip_size[chipname] > 800:
current_data = copy.deepcopy(self.index_assignments[chipname])
new_data = library_data['data']
current_data.extend(new_data)
ratio_sites, is_not_balance_list = self.count_barcode_radio(current_data)
if is_not_balance_list:
base_balance = False
if sizelimit and notrepeatbarcode and exclusive_classific and splibrary and base_balance:
return True
return False
def add_loc_num(self):
# 有nextera文库 必须满足大于50G
chipname = f'chip{self.loc_chip_num}'
nextera_size = self.chip_speciallib_nextera_size[chipname]
if nextera_size > 50 or nextera_size == 0:
self.loc_chip_num += 1
else:
# 有nextera文库但是不满足50G 去除
nextary_barcode = set()
no_nextary_data = list()
for libdata in self.index_assignments[chipname]:
if libdata['classification'].lower() != 'nextera':
no_nextary_data.append(libdata)
else:
self.no_assign_data.append(libdata)
nextary_barcode.update(libdata['barcode'])
self.index_assignments[chipname] = no_nextary_data
self.chip_barcode_recode[chipname] -= nextary_barcode
self.chip_speciallib_nextera_size[chipname] = 0
def assign_samples(self):
ori_library_data = list()
if '未测' not in self.ori_data.keys():
raise UserWarning('提供excel没有 未测 sheet ,请核查!')
ori_library_df = pd.DataFrame(self.ori_data['未测'])
# need_col = ['status', '#library', 'sublibrary', 'i5', 'i7', 'data_needed', 'real_data', 'customer',
# 'classification', 'priority', 'time', '拆分方式', 'barcode', 'is_balance_lib', '备注',
# 'TIPS1', 'TIPS2', 'TIPS3'
# ]
self.need_cols = self.read_cols()
get_col = set(ori_library_df.columns)
unhave_col = set(self.need_cols) - get_col
if unhave_col:
unhave_fom = '; '.join(unhave_col)
raise UserWarning(f'未测表里没有{unhave_fom} 表头,请核查!')
numeric_mask = pd.to_numeric(ori_library_df['data_needed'], errors='coerce').notna()
time_mask = pd.to_datetime(ori_library_df['time'], errors='coerce').notna()
# 添加处理status列的逻辑
status_mask = ori_library_df['status'] == '暂不排样'
ori_library_df['note'] = ''
ori_library_df.loc[~numeric_mask, 'note'] = 'data_needed 列非数字'
ori_library_df.loc[~time_mask, 'note'] = 'time 列非日期'
ori_library_df.loc[status_mask, 'note'] = '暂不排样'
# need_col.append('note')
no_ori_data = ori_library_df[~(numeric_mask & time_mask) | status_mask]
self.no_assign_data.extend(no_ori_data.to_dict('records'))
# 使用布尔索引筛选出不是数字和非日期的行
ori_library_df = ori_library_df[(numeric_mask & time_mask) & ~status_mask]
ori_library_df['level'] = ori_library_df.apply(self.level, axis=1)
# # 极致客户有重复的把等级调到0防止放到了最后到了未测里
# duplicate_name = ori_library_df[ori_library_df['level'] == 2].duplicated(subset='barcode', keep=False)
# # 将 'level' 列的值改为 0
# ori_library_df.loc[duplicate_name, 'level'] = 0
for library, library_df in ori_library_df.groupby('#library'):
size = library_df['data_needed'].sum()
# 文库内部有重复
if len(library_df['barcode'].values) > len(set(library_df['barcode'].values)):
library_df['note'] = '文库内部有重复'
library_df.loc[:, 'time'] = library_df['time'].apply(format_date)
self.no_assign_data.extend(library_df.to_dict('records'))
continue
flag = False
if size > (self.data_limit) / 2:
library_df['data_needed'] = library_df['data_needed'] / 2
flag = True
ori_library_data.append(dict(
library=library,
is_balance_lib=library_df['is_balance_lib'].values[0],
size=library_df['data_needed'].sum(),
split_method=library_df['拆分方式'].values[0],
time=library_df['time'].values[0],
level=library_df['level'].values[0],
customer=library_df['customer'].values[0],
classification=library_df['classification'].values[0],
data=library_df[self.need_cols].to_dict('records')
))
if flag:
self.return_log.append(f'文库{library} 已做拆分处理, 请注意!!! ')
ori_library_data.append(dict(
library=library,
is_balance_lib=library_df['is_balance_lib'].values[0],
size=library_df['data_needed'].sum(),
split_method=library_df['拆分方式'].values[0],
time=library_df['time'].values[0],
level=library_df['level'].values[0],
customer=library_df['customer'].values[0],
classification=library_df['classification'].values[0],
data=library_df[self.need_cols].to_dict('records')
))
ori_sort_data = sorted(ori_library_data, key=lambda x: (x['level'], x['time'], -x['size']))
i = 0
while ori_sort_data:
library_data = ori_sort_data[0]
chipname = f'chip{self.loc_chip_num}'
# 空白芯片直接添加
if chipname not in self.index_assignments:
self.add_new_data(chipname, library_data)
ori_sort_data.remove(library_data)
i += 1
continue
# 判断条件
if self.judge_data(chipname, library_data):
self.add_new_data(chipname, library_data, newer=False)
ori_sort_data.remove(library_data)
i += 1
else:
for j in range(len(ori_sort_data)):
newlibrary_data = ori_sort_data[j]
if self.judge_data(chipname, newlibrary_data):
ori_sort_data.remove(newlibrary_data)
i += 1
self.add_new_data(chipname, newlibrary_data, newer=False)
break
j += 1
else:
# self.loc_chip_num += 1
self.add_loc_num()
if self.chip_size[chipname] > self.data_limit:
# self.loc_chip_num += 1
self.add_loc_num()
def assign_again(self):
pass
def run(self):
# self.assign_samples()
try:
self.assign_samples()
except Exception as e:
self.return_log.append(f'T7排样出错 请联系!{e}')
self.index_assignments = {}
outputname = 'assignments_%s_%s' % (datetime.now().strftime("%m%d%H%M"), os.path.basename(self.path))
outputpath = os.path.join(self.output, 'result', outputname)
writer = pd.ExcelWriter(outputpath)
# ga = Ga(sheets=self.index_assignments)
# self.index_assignments = ga.run()
chip_loc = 1
librarynum = 0
for chip_idx, chip_assignments in self.index_assignments.items():
if not chip_assignments:
continue
df = pd.DataFrame(chip_assignments)
df['time'] = df['time'].dt.strftime('%Y-%m-%d')
if df['data_needed'].sum() < 1600 or librarynum > self.librarynum:
df['note'] = '排样数据量不足1600或者排样管数超标'
self.no_assign_data.extend(df.to_dict('records'))
continue
librarynum += len(set(df['#library'].values))
if [method for method in df['拆分方式'].values if '极致' in method]:
addname = 'X'
else:
addname = ''
self.dec_barcode_radio(chip_idx)
chipname = addname + chip_idx
sum_list = list()
for library, library_df in df.groupby('#library'):
sum_list.append(dict(
二次拆分=library,
客户=library_df['customer'].values[0],
类型=library_df['classification'].values[0],
打折前=library_df['data_needed'].sum()
))
df_sum = pd.DataFrame(sum_list)
res_df = pd.concat([df, df_sum], axis=1)
res_df.to_excel(writer, sheet_name=chipname, index=False)
chip_loc += 1
no_assign_df = pd.DataFrame(self.no_assign_data)
no_assign_df = no_assign_df.applymap(lambda x: format_date(x) if isinstance(x, pd.Timestamp) else x)
no_assign_df = no_assign_df[self.need_cols]
no_assign_df.to_excel(writer, sheet_name='未测', index=False)
if self.return_log:
pd.DataFrame(self.return_log).to_excel(writer, sheet_name='log', index=False)
writer.close()
return outputpath
if __name__ == '__main__':
start_time = time.time()
filepath = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'example', 'input排样表.xlsx')
# excel_file = 'example/input排样表.xlsx'
output_file = ''
layout = AutoLayout(filepath, output_file)
layout.run()
end_time = time.time()
execution_time = end_time - start_time
print(f"代码执行时间为:{execution_time}")
# server()