Tag: bioinformatics

Creating a list of positions of a substring within a string (DNA) (Python 3)

bioinformatics indexing python string substring

I am doing a bioinformatics course and I am trying to write a function to find all occurrences of a substring within a string. The output above should exactly match the following: [2, 4, 10] [2, 5, 6, 15, 17, 18] How can I fix this? Preferably without using regular expressions. Answer It looks like you badly indented the code,

regex for finding gene product from the text

bioinformatics python regex

What regex should I use for matching such text by far I have tired this pattern: Answer Use See regex proof. EXPLANATION

Fill dataframe values per column, by row index, if position is present in range

bioinformatics pandas python python-3.x

I have a list of start and stop coordinates of ranges and would like to fill a pandas df according to their being present in a range. The numbers of rows are predetermined and filled with ‘0’. If for example a range is 1,3 for a column then rows (index) 1-3 would be filled with ‘1’. This is hugely inefficient

OneHotEncoding Protein Sequences

bioinformatics one-hot-encoding python scikit-learn

I have an original dataframe of sequences listed below and am trying to use one-hot encoding and then store these in a new dataframe, I am trying to do it with the following code but am not able to store because I get the following output afterwards: Code: but get error Answer You get that strange array because it treats

Python and Matplotlib: characters as the x axis

bioinformatics matplotlib pandas python

Hi Stack Overflow community. I think I am trying to code the impossible with matplotlib, so if there is a different python library that will better suit me, please let me know! I have an entire amino acid sequence (Represented as capital letters in the image) of a protein (protein x). This will be my x axis. I have two

How to make a nested for loop using a generator in python?

bioinformatics generator nested python syntax

I’m trying to convert this nested for loop: to a one liner, something like this: But I’m getting this error: all_R is a defaultdict where every value has keys that are pairs, and I’m interested in just one value from that pair: Answer List comprehensions are written in the same order as for loops, so you are actually looking for

Python: How to encode DNA sequence using binary values?

bioinformatics biopython encoding python sequence

I would like to convert a file that contained few DNA sequences into binary values which is as follow: FileA.txt Desired output I have tried using this code to solve my problem but the bin output file seem failed to output my desired answer. Can anyone help me? Code Answer Do you want ascii output or binary? The below will