通过一个公共列python将两个txt文件合并在一起答案

【问题标题】：merge two txt files together by one common column python通过一个公共列python将两个txt文件合并在一起
【发布时间】：2014-12-04 21:35:59
【问题描述】：

如何读入两个制表符分隔的文件 .txt 并将它们映射到一个公共列。

例如，从这两个文件中创建基因到通路的映射：

第一个文件，pathway.txt

 Pathway                                                Protein
 Binding and Uptake of Ligands by Scavenger Receptors   P69905                                          
 Erythrocytes take up carbon dioxide and release oxygen P69905                                         
 Metabolism                                             P69905
 Amyloids                                               P02647
 Metabolism                                             P02647
 Hemostasis                                             P68871

第二个文件，gene.txt

 Gene   Protein
 Fabp3  P11404
 HBA1   P69905
 APOA1  P02647
 Hbb-b1 P02088
 HBB    P68871
 Hba    P01942

输出会是这样的，

 Gene  Protein     Pathway
 Fabp3  P11404     
 HBA1   P69905     Binding and Uptake of Ligands by Scavenger Receptors, Erythrocytes take up carbon dioxide and release oxygen, Metabolism
 APOA1  P02647     Amyloids, Metabolism
 Hbb-b1 P02088
 HBB    P68871     Hemostasis
 Hba    P01942

如果没有通路对应于蛋白质 id 信息的基因碱基，则留空。

更新：

 import pandas as pd

 file1= pd.read_csv("gene.csv")
 file2= pd.read_csv("pathway.csv")

 output = pd.concat([file1,file2]).fillna(" ")
 output= output[["Gene","Protein"]+list(output.columns[1:-1])]
 output.to_csv("mapping of gene to pathway.csv", index=False)

所以这只给了我我不期望的合并文件。

【问题讨论】：

从哪里摄取配体............来自哪里？？？
@Hackaholic 刚刚修正了错字。
@abs27 试着写一些代码。如果您遇到任何错误，我们会为您提供帮助。
@BhargavRao 我打算用熊猫。
@abs27 继续您的计划，完成一些工作并发布代码。如果您遇到任何错误，我们将帮助您调试它，否则，将其发布为答案，我们都会从中吸取教训。

标签： python pandas

【解决方案1】：

>>> from collections import defaultdict
>>> my_dict = defaultdict()
>>> f = open('pathway.txt')
>>> for x in f:
...     x = x.strip().split()
...     value,key = " ".join(x[:-1]),x[-1]
...     if my_dict.get(key,0)==0:
...         my_dict[key] = [value]
...     else:my_dict[key].append(value)
... 
>>> my_dict
defaultdict(None, {'P68871': ['Hemostasis'], 'Protein': ['Pathway'], 'P69905': ['Binding', 'Erythrocytes', 'Metabolism'], 'P02647': ['Amyloids', 'Metabolism']})
>>> f1 = open('gene.txt')
>>> for x in f1:
...     value,key = x.strip().split()
...     if my_dict.get(key,0)==0:
...         print("{:<15}{:<15}".format(value,key))
...     else: print("{:<15}{:<15}{}".format(value,key,", ".join(my_dict[key])))
... 
Gene           Protein        Pathway
Fabp3          P11404         
HBA1           P69905         Binding and Uptake of Ligands by Scavenger Receptors,  Erythrocytes take up carbon dioxide and release oxygen Metabolism
APOA1          P02647         Amyloids, Metabolism
Hbb-b1         P02088         
HBB            P68871         Hemostasis
Hba            P01942

【讨论】：

【解决方案2】：

class Protein:

    def __init__(self, protein, pathway = None, gene = ""):
        self.protein = protein
        self.pathways = []
        self.gene = gene

        if pathway is not None:
            self.pathways.append(pathway)
        return

    def __str__(self):
        return "%s\t%s\t%s" % (
            self.gene, 
            self.protein, 
            ", ".join([p for p in self.pathways]))      

# protein -> pathway map
proteins = {}

# get the pathways
f1 = file("pathways.txt")
for line in f1.readlines()[1:]: 
    tokens = line.split()
    pathway = " ".join(tokens[:-1])
    protein = tokens[-1]

    if protein in proteins:
        p = proteins[protein]
        p.pathways.append(pathway)
    else:
        p = Protein(protein = protein, pathway = pathway)
        proteins[protein] = p

# get the genes
f2 = file("genes.txt")
for line in f2.readlines()[1:]:
    gene, protein = line.split()

    if protein in proteins:
        p = proteins[protein]    
        p.gene = gene
    else:
        p = Protein(protein = protein, gene = gene)
        proteins[protein] = p

# print the results
print "Gene\tProtein\tPathway"
for protein in proteins.values():
    print protein

【讨论】：