将邻接矩阵转换为csv文件 [英] Convert adjacency matrix to a csv file

问题描述

我想使用python（或可能的R）将ARACNE的邻接矩阵输出转换为csv文件。

I want to convert the adjacency matrix output from ARACNE into a csv file using python (or possibly R).

adj文件设置为显示一个基因一个正确和每一个与其他基因的相互作用。例如：

The adj file is set up to show one gene one the right and each of its interactions with other genes. For example:

A B 0.4 C 0.3
B C 0.1 E 0.4
C D 0.2 E 0.3

如上所述，A和B互相交互，交互的值为0.4。 A和C彼此交互，值为0.3，以此类推。

So above, A and B interact with each other and the value of that interaction is 0.4. A and C interact with each other and the value is 0.3 and so on.

我要更改布局，以便我...

I want to change the layout so I get...

A B 0.4
A C 0.3
B C 0.1
B E 0.4
C D 0.2
C E 0.3

基本上，我想要一个所有交互节点和相应的值的列表，以便我可以将文件上传到Cytoscape并绘制网络。

Basically I want a list of all interacting nodes and the corresponding values so that I can upload the file to Cytoscape and plot a network.

推荐答案

一个简单的方法使用 csv p>

A simple way to do this using csv module -

import csv
with open('<inputfile>','r') as f , open('<outputfile>','w') as of:
    reader = csv.reader(f, delimiter=' ')
    writer = csv.writer(of, delimiter=' ')
    for lines in reader:
            key = lines.pop(0)
            for i in range(0,len(lines),2):
                    writer.writerow([key, lines[i], lines[i+1]])

---

示例/ Demo -

---

Example/Demo -

我的 a.csv -

A B 0.4 C 0.3
B C 0.1 E 0.4
C D 0.2 E 0.3

代码 -

>>> import csv
>>> with open('a.csv','r') as f , open('b.csv','w') as of:
...     reader = csv.reader(f, delimiter=' ')
...     writer = csv.writer(of, delimiter=' ')
...     for lines in reader:
...             key = lines.pop(0)
...             for i in range(0,len(lines),2):
...                     writer.writerow([key, lines[i], lines[i+1]])

输出在 b.csv -

A B 0.4
A C 0.3
B C 0.1
B E 0.4
C D 0.2
C E 0.3

这篇关于将邻接矩阵转换为csv文件的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！