kmers | packed k-mer representation | Genomics library

I have a list of pandas data frames that I got applying the groupby function and I want to add to them a new column with the frequency of each kmer. I did that with a loop but I got a message warning that I need to use df.loc[index, col_names]. Here it is a link to one example of the csv file: https://drive.google.com/file/d/17vYbIEza7l-1mFnavGGO1QjCjPdhxG7C/view?usp=sharing

I have stuck with this script it would be great if you could help me with your inputs. My problem is that I think the script is not that efficient - it takes a lot of time to end running.

I have a fasta file with around 9000 sequence lines (example below) and What my script does is:

1. reads the first line (ignores lines start with >) and makes 6mers (6 character blocks)
2. adds these 6mers to a list
3. makes reverse-complement of previous 6mers (list2)
4. saves the line if non of the reverse-complement 6mers are in the line.
5. Then goes to the next line in the file, and check if it contains any of the reverse-complement 6mers (in list2). If it does, it discards it. If it does not, it saves that line, and reads all reverse complement 6-mers of the new one into the list2 - in addition to the reverse-complement 6-mers that were already there.

my file:

I have a dataframe my_data which looks like this:

I have made a recursive program to find set of all possible strings made of certain characters. Here set of characters are - A,C,G,T,-. I am not able to find the reason for the memory error and want to improve the logic.

Hello I have a dataframe which looks like this:

The function compute_kmers tries to find how many times a substring kmer occurs in string reference_string, k is the lengh of kmer. This works on very small inputs, but on large one it finds different and wrong results. Can't sure what I am doing wrong.

Got this function, which generates all possible kmers over the four Bases in python:

This code needs to find the most frequent k-mers (substrings of k letters) with d mismatches in a string (genome). In the past I had to find the most frequent k-mer without mismatches and I'm trying minimally alter my code. To do so, I would have to be able to increment values in a dictionary that have a different key from a string I'm passing. Is that possible? Below is my code. Is there a way to do what I have written in the comment? HammingDistance() just computes the number of differences between 2 strings.

I am trying to use the return value fileName from the method file(), to the method nGram() so I can parse the contents of the file into n-grams. I have working code to do this but I want have two seperate methods.