Collapse a set of redundant kmers to use IUPAC degenerate bases

Last update: Jan 06, 2022

Overview

kmer-collapse

Collapse a set of redundant kmers to use IUPAC degenerate bases

Overview

Given an input set of kmers, find the smallest set of kmers that encapsulates all diversity in the input set using IUPAC degenerate bases. This aims to solve the problem described here: https://www.biostars.org/p/9498272/

Usage

Install the marisa-trie library, if necessary.

Modify the script's input variable to specify desired sequences, and then run the script:

$ python kmer-collapse.py
{
    "input": [
        "AAAAAAAAAA",
        "TAAAAAAAAA",
        "ACAAAAAAAA",
        "AGAAAAAAAA"
    ],
    "encoded_output": [
        "WAAAAAAAAA",
        "ASAAAAAAAA"
    ]
}

Notes

This has not been tested with any kmer sets but those examples provided. However, it aims to be scalable by pruning combinations of sub-kmers along the way, which would otherwise yield incorrect encodings. This also uses a trie for faster prefix testing. If futher performance is needed, some easy wins would be to cache sub-kmer tests, since most of these test outcomes would be redundant.

Additionally, no error checking is done on the input kmer alphabet or on the consistency of kmer lengths. It may be useful to validate input before using this script.

Examples

These examples are available from the script by uncommenting the relevant input.

A

{
    "input": [
        "AAAAAAAAAA",
        "TAAAAAAAAA"
    ],
    "encoded_output": [
        "WAAAAAAAAA"
    ]
}

B

{
    "input": [
        "AAAAAAAAAA",
        "TAAAAAAAAA",
        "GCGAAAAAAA"
    ],
    "encoded_output": [
        "GCGAAAAAAA",
        "WAAAAAAAAA"
    ]
}

C

{
    "input": [
        "AAAAAAAAAA"
    ],
    "encoded_output": [
        "AAAAAAAAAA"
    ]
}

D

{
    "input": [
        "AAAAAAAAAA",
        "TAAAAAAAAA",
        "CAAAAAAAAA",
        "GAAAAAAAAA"
    ],
    "encoded_output": [
        "NAAAAAAAAA"
    ]
}

E

{
    "input": [
        "AAAAAAAAAA",
        "TAAAAAAAAA",
        "TTAAAAAAAA",
        "ATAAAAAAAA"
    ],
    "encoded_output": [
        "WWAAAAAAAA"
    ]
}

F

{
    "input": [
        "AAAAAAAAAA",
        "TAAAAAAAAA",
        "CAAAAAAAAA",
        "GAAAAAAAAA",
        "TACAGATACA",
        "AACAGAAAAA"
    ],
    "encoded_output": [
        "NAAAAAAAAA",
        "TACAGATACA",
        "AACAGAAAAA"
    ]
}

G

{
    "input": [
        "AAAAAAAAAA",
        "TAAAAAAAAA",
        "ACAAAAAAAA",
        "AGAAAAAAAA"
    ],
    "encoded_output": [
        "ASAAAAAAAA",
        "WAAAAAAAAA"
    ]
}

Collapse a set of redundant kmers to use IUPAC degenerate bases

Related tags

Overview

kmer-collapse

Overview

Usage

Notes

Examples

A

B

C

D

E

F

G

Owner

Alex Reynolds

Backup dc registry - A simple POC that abuses Backup Operator privileges to remote dump SAM, SYSTEM, and SECURITY

Source code for Learn Programming: Python

Get a list of the top-10 rejected libraries in your WhiteSource inventory

Defichain maxi - Scripts to optimize performance on defichain rewards

Educational Repo. Used whilst learning Flask.

A nonebot2 plugin, send news information in a picture form.

Скрипт позволяет выгрузить участников чатов/каналов(по чату для комментариев) и сообщения в различные форматы файлов.

Repo contains Python Code Reference to learn Python in a week, It also contains Machine Learning Algorithms and some examples for Practice, Also contains MySql, Tableau etc

The git for the Python Story Utility Package library.

log4shell pwner for vulnerable minecraft servers

An alternative app for core Armoury Crate functions.

School helper, helps you at your pyllabus's.

This wishes a mentioned users on their birthdays

This program goes thru reddit, finds the most mentioned tickers and uses Vader SentimentIntensityAnalyzer to calculate the ticker compound value.

Banking management project using Tkinter GUI in python.

Analyzes crypto candles over a set time period and then trades based on winning patterns found

Pacman - A suite of tools for manipulating debian packages

A minimalist starknet amm adapted from StarkWare's amm.

An unofficial opensource Pokemon cursor theme for Windows and Linux.

Cross-platform .NET Core pre-commit hooks