DiscountPy : k-mer counting tool

Contents:

• Requirements
• Setup
• Some codes

Requirements

1. DiscountPy is completely Python based. To run it on your machine, python >= 3.9 is required.
   
2. Poetry is a tool for dependency management and packaging in Python. Make sure to install it.
   
3. Try to run all the commands in Powershell

Setup

1. Installation: You can download the zip file or clone it.

2. Setting up: First install all the dependencies and create virtual environment. To do so, run the following commands in workspace terminal.

   poetry install
   poetry update
   

3. Now configure python interpreter. For configuring, first get the env path. To get the env information, run the following command.

   poetry env info
   

   • Or to know only path, run

     poetry env info --path
     

To know more about poetry, follow Poetry

Now DiscountPy is ready to be run.

Some codes

DiscountPy is a k-mer counting tool, it gives you three orderings for counting the k-mers.

• -k : Length of the k-mer
• -m : Width of the minimizers
• -f : Input dataset (.fasta)
• -o : Order (lex | freq)
• --minimizers : Universal minimizer set

How to use?

1. To get the hashed super-mers with minimizers

   • By lexicographically ordered

     discount -k 28 -o lex -f data/SRR094926.fasta 
     

     or

     discount -k 28 -m 10 lex -f data/SRR094926.fasta
     

   • By frequency ordering

     discount -k 28 -f data/SRR094926.fasta
     

     or you can skip the -o in frequency order as default value is -o freq

     discount -k 28 -o freq -f data/SRR094926.fasta
     

   • By universal frequency ordering

     discount -k 28 -f data/SRR094926.fasta --minimizers PASHA/pasha_all_28_10.txt
     

     or

     discount -k 28 -o freq -f data/SRR094926.fasta --minimizers PASHA/pasha_all_28_10.txt
     

2. To generate file of the hashed super-mers:

   discount -k 28 -o freq -f data/SRR094926.fasta --minimizers PASHA/pasha_all_28_10.txt --output output/xxx.txt
   

3. At finally getting the counts of the k-mers:

   • You have to sort the above generated file externally and input that file.

     discount -k 28 -f sortedXYZ.txt --count directory/to/counted-kmer-file
     

Query