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bug修复

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chaopower 2023-08-01 18:09:34 +08:00
parent 8244373e21
commit cc63ef71e5
3 changed files with 6 additions and 4 deletions
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10
tools/parsexlsx.py
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@ -50,8 +50,9 @@ class Parse(BaseAssignment):
if data.empty: if data.empty:
self.result['snvindel'] = res self.result['snvindel'] = res
return return
data['freq'] = data['mutant_frequency'].apply(lambda x: float(x.replace('%', '')))
data = data[data['Validated'] == 1].reset_index() # 去除不可信，vus中的 %2以下的突变
data = data[data['Validated'] == 1 & (~((data['freq'] < 2) & (data['AMP_mut_level'] == 'III')))].reset_index()
data['muttype'] = '/' data['muttype'] = '/'
data.loc[data['ExonicFunc.refGene'].str.match('nonsynonymous SNV'), 'muttype'] = '错义突变' data.loc[data['ExonicFunc.refGene'].str.match('nonsynonymous SNV'), 'muttype'] = '错义突变'
data.loc[data['ExonicFunc.refGene'].str.match('^frameshift'), 'muttype'] = '移码突变' data.loc[data['ExonicFunc.refGene'].str.match('^frameshift'), 'muttype'] = '移码突变'
@ -79,7 +80,8 @@ class Parse(BaseAssignment):
# 汇总 # 汇总
if alter_res['AMP_mut_level'] in ['I', 'II']: if alter_res['AMP_mut_level'] in ['I', 'II']:
self.signtb.add(alter) self.signtb.add(alter)
self.sign_from_type['target'][alter_res['gene']] = '%s %s' % (alter_res['gene'], alter_res['nacid']) self.sign_from_type['target'][alter_res['gene']] = '%s(%s)' % (
alter_res['aacid'], alter_res['mutant_frequency'])
self.result['snvindel'] = res self.result['snvindel'] = res
@ -424,7 +426,7 @@ class Parse(BaseAssignment):
self.signdurg.update(set(drug_category_alter_data_split['drug_split'].tolist())) self.signdurg.update(set(drug_category_alter_data_split['drug_split'].tolist()))
drug_category_alter_data_split['drugdes'] = drug_category_alter_data_split.apply( drug_category_alter_data_split['drugdes'] = drug_category_alter_data_split.apply(
lambda x: '%s 【%s 级】' % (x['drug_split'], x['AMP_evidence_level']), axis=1) lambda x: '%s 【%s 级】' % (x['drug_split'], x['AMP_evidence_level']), axis=1)
drug_category_res[drug_category] = '\n'.join(drug_category_alter_data_split['drugdes'].to_list()) drug_category_res[drug_category] = '\n'.join(set(drug_category_alter_data_split['drugdes'].to_list()))
# 所有药物信息 # 所有药物信息
groupdata['list_col'] = groupdata['DrugCn'].str.replace(' + ', '+').str.split(r'[+,]') groupdata['list_col'] = groupdata['DrugCn'].str.replace(' + ', '+').str.split(r'[+,]')