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

Tools, guides, and resources for blockchain analysts to interface with data on the Ergo platform.

Install JetBrains Toolbox

Nextstrain build targeted to Omicron

Convex Optimisation MVA course - Assignment

This repository collects nice scripts ("plugins") for the SimpleBot bot for DeltaChat.

A redesign of our previous Python World Cup, aiming to simulate the 2022 World Cup all the way from the qualifiers

Developing a python based app prototype with KivyMD framework for a competition :))

The functions we created are included in a script. The necessary parts for pre-processing were taken. Analysis complete.

A demo Piccolo app - a movie database!

Python client SDK designed to simplify integrations by automating key generation and certificate enrollment using Venafi machine identity services.

Generate PNG filles from NFO files.

A python module for DeSo

XlvnsScriptTool - Tool for decompilation and compilation of scripts .SDT from the visual novel's engine xlvns

Tuple-sum-filter - Library to play with filtering numeric sequences by sums of their pairs, triplets, etc. With a bonus CLI demo

SpellingBeeSolver - This program generates solutions to NYT style spelling bee problems.

Neptune client library - integrate your Python scripts with Neptune

Bootstraparse is a personal project started with a specific goal in mind: creating static html pages for direct display from a markdown-like file

A little tool that uses LLVM to extract simple "what does this do" level instruction information from all architectures.

reproduces experiments from

Sailwind Mod Manager