合并两个熊猫数据帧，并在由管道分隔的列中输入匹配的条目

问题描述

在列variants上的数据框之间映射时，我有2个大熊猫数据框phenotype和gene，它应该打印变体数据框的所有行，并用新列HP-ID隔开， pipe。这是数据框的几行

import pandas

# variants

data_var = {'CHROM': ['Chr1','Chr11'],'START': [51937273,56867846],'GENE': ['KCNJ1','NPHS2'],'REF': ['C','G'],'ALT': ['T','A']}

variants = pd.DataFrame(data_var)

   CHROM     START   GENE REF ALT
0   Chr1  51937273  KCNJ1   C   T
1  Chr11  56867846  NPHS2   G   A

# phenotype

data_phe = {'entrez-id': [3758,3758,7827,7827],'KCNJ1','NPHS2','HP-ID': ['HP:0002013','HP:0002007','HP:0001561','HP:0000256','HP:0001508','HP:0003774','HP:0003678','HP:0000093','HP:0003073'],'phenotype': ['Vomiting','Frontal bossing','Polyhydramnios','Macrocephaly','Failure to thrive','Stage 5 chronic kidney disease','Rapidly progressive','Proteinuria','Hypoalbuminemia']}


phenotype = pd.DataFrame(data_phe)

   entrez-id   GENE       HP-ID                       phenotype
0       3758  KCNJ1  HP:0002013                        Vomiting
1       3758  KCNJ1  HP:0002007                 Frontal bossing
2       3758  KCNJ1  HP:0001561                  Polyhydramnios
3       3758  KCNJ1  HP:0000256                    Macrocephaly
4       3758  KCNJ1  HP:0001508               Failure to thrive
5       7827  NPHS2  HP:0003774  Stage 5 chronic kidney disease
6       7827  NPHS2  HP:0003678             Rapidly progressive
7       7827  NPHS2  HP:0000093                     Proteinuria
8       7827  NPHS2  HP:0003073                 Hypoalbuminemia

所需的输出

CHROM  START  GENE  REF  ALT  HP-ID
Chr1  51937273  KCNJ1  C  T  HP:0002013|HP:0002007|HP:0001561|HP:0000256|HP:0001508
Chr6  56867846  NPHS2  G  A  HP:0003774|HP:0003678|HP:0000093|HP:0003073

我累了

data_frames = [variants,phenotype]
df_marged = reduce(lambda left,right: pd.merge(left,right,on=['GENE'],how='outer'),data_frames)

这会打印出所有变体和表型的行，当它们在另一行之下匹配时。

解决方法

首先由GroupBy.agg汇总join，然后使用DataFrame.merge：

variants.merge(phenotype.groupby('GENE')['HP-ID'].agg('|'.join).reset_index(),on='GENE')