bug 更新
parent
1bffac2029
commit
c60d5fe6cc
17
T7_server.py
17
T7_server.py
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@ -67,16 +67,23 @@ def server():
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adrss = ("", 8191)
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myserver.bind(adrss)
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myserver.listen(5)
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while True:
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try:
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myclient, adddr = myserver.accept()
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recv_content, chipnum = recvdata(myclient, os.path.join(basedir, 'example'))
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layout = T7(recv_content, chipnum)
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outputpath = layout.run()
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senddata(myclient, outputpath)
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except Exception as e:
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print(e)
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continue
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# while True:
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# try:
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# myclient, adddr = myserver.accept()
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# recv_content, chipnum = recvdata(myclient, os.path.join(basedir, 'example'))
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# layout = T7(recv_content, chipnum)
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# outputpath = layout.run()
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# senddata(myclient, outputpath)
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# except Exception as e:
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# print(e)
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# continue
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if __name__ == '__main__':
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95
tools/t7.py
95
tools/t7.py
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@ -13,7 +13,7 @@ class AutoLayout:
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自动化派样
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"""
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def __init__(self, path, chipnum, output=basedir, data_limit=1520):
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def __init__(self, path, chipnum, output=basedir, data_limit=1800):
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self.path = path
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self.output = output
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self.chipnum = int(chipnum)
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@ -78,39 +78,39 @@ class AutoLayout:
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self.chip_customer[chipname].add(library_data['customer'])
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self.chip_classification[chipname].add(library_data['classification'])
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def add_new_chip(self, library_data):
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"""
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要新增到芯片上的数据
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:param library_data:
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:return:
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"""
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chip_num_tmp = self.loc_chip_num
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while True:
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chip_num_tmp += 1
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chipname_tmp = f'chip{chip_num_tmp}'
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library = library_data['library']
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if chipname_tmp not in self.index_assignments:
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self.logger.error(f'{library} {chipname_tmp} 常规添加')
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self.add_new_data(chipname_tmp, library_data)
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break
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else:
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is_same_barcode = self.chip_barcode_recode[chipname_tmp].intersection(
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{item['barcode'] for item in library_data['data']})
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# 没有从重复的index,并且也不互斥的
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if ((self.chip_size[chipname_tmp] + library_data['size']) > self.data_limit):
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self.logger.error(f'{library} {chipname_tmp} 文库相加大于设定限制')
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if ((self.chip_speciallib_size[chipname_tmp] + library_data['size']) >= 200):
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self.logger.error(f'{library} {chipname_tmp} 不平衡文库相加大于设定限制')
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if is_same_barcode:
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self.logger.error(f'{library} {chipname_tmp} 文库有barcode重复')
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if self.use_rule(chipname_tmp, library_data['customer']):
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self.logger.error(f'{library} {chipname_tmp} 有互斥单位')
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if ((self.chip_size[chipname_tmp] + library_data['size']) <= self.data_limit) \
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and ((self.chip_speciallib_size[chipname_tmp] + library_data['size']) < 200) \
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and (not is_same_barcode) \
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and (not self.use_rule(chipname_tmp, library_data['customer'])):
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self.add_new_data(chipname_tmp, library_data, newer=False)
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break
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# def add_new_chip(self, library_data):
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# """
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# 要新增到芯片上的数据
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# :param library_data:
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# :return:
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# """
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# chip_num_tmp = self.loc_chip_num
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# while True:
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# chip_num_tmp += 1
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# chipname_tmp = f'chip{chip_num_tmp}'
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# library = library_data['library']
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# if chipname_tmp not in self.index_assignments:
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# self.logger.error(f'{library} {chipname_tmp} 常规添加')
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# self.add_new_data(chipname_tmp, library_data)
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# break
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# else:
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# is_same_barcode = self.chip_barcode_recode[chipname_tmp].intersection(
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# {item['barcode'] for item in library_data['data']})
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# # 没有从重复的index,并且也不互斥的
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# if ((self.chip_size[chipname_tmp] + library_data['size']) > self.data_limit):
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# self.logger.error(f'{library} {chipname_tmp} 文库相加大于设定限制')
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# if ((self.chip_speciallib_size[chipname_tmp] + library_data['size']) >= 200):
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# self.logger.error(f'{library} {chipname_tmp} 不平衡文库相加大于设定限制')
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# if is_same_barcode:
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# self.logger.error(f'{library} {chipname_tmp} 文库有barcode重复')
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# if self.use_rule(chipname_tmp, library_data['customer']):
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# self.logger.error(f'{library} {chipname_tmp} 有互斥单位')
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# if ((self.chip_size[chipname_tmp] + library_data['size']) <= self.data_limit) \
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# and ((self.chip_speciallib_size[chipname_tmp] + library_data['size']) < 200) \
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# and (not is_same_barcode) \
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# and (not self.use_rule(chipname_tmp, library_data['customer'])):
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# self.add_new_data(chipname_tmp, library_data, newer=False)
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# break
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def dec_barcode_radio(self, chipname):
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data = self.index_assignments[chipname]
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@ -134,8 +134,6 @@ class AutoLayout:
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# is_need_base = col_df.index[col_df['ratio'] < 0.088]
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A, B, C, D = list(), list(), list(), list(),
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need_base_list = list()
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ratio = col_df['ratio'].to_dict()
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for decbase in ['A', 'T', 'C', 'G']:
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if decbase not in ratio:
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@ -153,7 +151,7 @@ class AutoLayout:
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'%s 第%s位置,有碱基不平衡，算出结果为 %s' % (chipname, i, ratio)
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)
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if len(is_not_balance_list) > 2:
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if len(is_not_balance_list):
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self.return_log.append('有碱基不平衡性！')
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self.return_log.extend(is_not_balance_list)
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print('有碱基不平衡性！\n', '\n'.join(is_not_balance_list))
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@ -229,7 +227,7 @@ class AutoLayout:
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# 不平衡文库大于200G 不能添加
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splibrary = True
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if classification in ['扩增子', '不平衡文库', '单细胞文库', '甲基化'] \
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and self.chip_speciallib_size[chipname] + size > 200:
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and self.chip_speciallib_size[chipname] + size > 250:
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splibrary = False
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self.logger.error(f'{library} {chipname} 不平衡文库相加大于设定限制')
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if sizelimit and notrepeatbarcode and exclusive_classific and splibrary:
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@ -262,11 +260,12 @@ class AutoLayout:
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need_col.append('note')
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self.no_assign_data.extend(ori_library_df[~(numeric_mask & time_mask)].to_dict('records'))
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# 使用布尔索引筛选出不是数字和非日期的行
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ori_library_df = ori_library_df[numeric_mask & time_mask]
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ori_library_df['level'] = ori_library_df.apply(self.level, axis=1)
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no_ori_data = ori_library_df[~(numeric_mask & time_mask)]
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self.no_assign_data.extend(no_ori_data.to_dict('records'))
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# 使用布尔索引筛选出不是数字和非日期的行
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ori_library_df = ori_library_df[(numeric_mask & time_mask)]
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ori_library_df['level'] = ori_library_df.apply(self.level, axis=1)
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for library, library_df in ori_library_df.groupby('#library'):
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ori_library_data.append(dict(
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library=library,
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@ -308,14 +307,13 @@ class AutoLayout:
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j += 1
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else:
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self.loc_chip_num += 1
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if self.chip_size[chipname] > 1500:
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if self.chip_size[chipname] > self.data_limit:
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self.loc_chip_num += 1
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def assign_again(self):
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pass
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def run(self):
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self.assign_samples()
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try:
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self.assign_samples()
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except Exception as e:
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@ -328,17 +326,20 @@ class AutoLayout:
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chip_loc = 1
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for chip_idx, chip_assignments in self.index_assignments.items():
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df = pd.DataFrame(chip_assignments)
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if df['data_needed'].sum() < 1400 or chip_loc > self.chipnum:
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df['time'] = df['time'].dt.strftime('%Y-%m-%d')
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if df['data_needed'].sum() < 1500 or chip_loc > self.chipnum:
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self.no_assign_data.extend(chip_assignments)
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continue
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if '极致' in df['拆分方式'].values:
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if [method for method in df['拆分方式'].values if '极致' in method]:
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addname = 'X'
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else:
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addname = ''
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self.dec_barcode_radio(chip_idx)
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df.to_excel(writer, sheet_name=addname + chip_idx, index=False)
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chip_loc += 1
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pd.DataFrame(self.no_assign_data).to_excel(writer, sheet_name='未测', index=False)
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no_assign_df = pd.DataFrame(self.no_assign_data)
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# no_assign_df['time'] = no_assign_df['time'].dt.strftime('%Y-%m-%d')
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no_assign_df.to_excel(writer, sheet_name='未测', index=False)
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if self.return_log:
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pd.DataFrame(self.return_log).to_excel(writer, sheet_name='log', index=False)
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writer.close()
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