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Bioinformatics Programming

How to search for a specific character in a file using Python?

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python programming

In this article, a simple python script is provided that can be used to search for a specific character in a file.

If you have a file consisting of some information including name, address, email, post, and so on. You want to extract only email addresses present in that file, then use the following script/block of code. Here, this input file is named “employee_info.txt”.

#!/usr/bin/env python


value = ''
str = 'Email ID:'

file = open('employee_info.txt')

result = ''
for line in file:
			if '@' in line:				#looking for specific character
				value = line.splitlines()
				print ("Email ID:", value)
file.close()				

Save this script with .py extension. Suppose, save it as ‘script.py’. Open a terminal on Ubuntu or command prompt on Windows and type:

$ python script.py

If you want to redirect the output to a file, then type:

$ python script.py > output.txt

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Bioinformatics Programming

tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.

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tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.

RDKit [1] is a very nice cheminformatics software. It allows us to perform a wide range of operations on chemical compounds/ ligands. We have provided a Python script to perform fingerprinting using Tanimoto similarity on multiple compounds using RDKit. (more…)

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Bioinformatics Programming

How to commit changes to GitHub repository using vs code?

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How to commit changes to GitHub repository using vs code?

In this article, we are providing a few commands that are used to commit changes to GitHub repositories using VS code terminal.

(more…)

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Bioinformatics Programming

Extracting first and last residue from helix file in DSSP format.

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Extracting first and last residue from helix file in DSSP format.

Previously, we have provided a tutorial on using dssp_parser to extract all helices including long and short separately. Now, we have provided a new python script to find the first and last residue in each helix file. (more…)

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