https://github.com/ulelab/cluster_kmers

Get clusters of k-mers based solely on their sequence or in combination with enrichment in PEKA.
https://github.com/ulelab/cluster_kmers

Last synced: 5 months ago
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Get clusters of k-mers based solely on their sequence or in combination with enrichment in PEKA.

• Host: GitHub
• URL: https://github.com/ulelab/cluster_kmers
• Owner: ulelab
• License: gpl-3.0
• Created: 2023-02-22T15:04:05.000Z (over 3 years ago)
• Default Branch: master
• Last Pushed: 2023-11-21T09:16:28.000Z (over 2 years ago)
• Last Synced: 2025-09-05T04:12:02.115Z (10 months ago)
• Language: Python
• Size: 1.29 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

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README

          
# cluster_kmers

[![DOI](https://zenodo.org/badge/605154452.svg)](https://zenodo.org/badge/latestdoi/605154452)

Get clusters of k-mers based solely on their sequence or in combination with enrichment in PEKA. 

## Installation

```

conda create -n cluster_kmers

conda activate cluster_kmers

# Python must be >=3.8 or <=3.11 to support SciPy 1.9

conda install python=3.9 pip

pip install git+https://github.com/ulelab/cluster_kmers.git@master

```

## Usage

```

cluster_kmers [-h] -k KMERS [KMERS ...] -o RESULTS_FOLDER [-co {seq,seq_enrichment}] [-n N_CLUSTERS] [-peka PEKA_FILES [PEKA_FILES ...]] [-tl MIN_TOKEN_LENGTH] [-wl {True,False}] [-cons CONSENSUS_LENGTH]

```

Cluster k-mers based on sequence or on a combination of sequence and enrichment in CLIP data.

```

required arguments:

  -k KMERS [KMERS ...], --kmers KMERS [KMERS ...]

                        A list of k-mers encoded in RNA alphabet separated by spaces: AAGG GGAG GCCU.

  -o RESULTS_FOLDER, --output_folder RESULTS_FOLDER

                        A path to an existing output folder, for example "~/results"

optional arguments:

  -co {seq,seq_enrichment}, --cluster_on {seq,seq_enrichment}

                        Inputs to clustering. Valid options are: seq - Cluster only based on sequence similarity. seq_enrichment - Cluster based on sequence similarity and based on enrichment of motifs in CLIP data (this option requires arguments passed to -peka)

  -n N_CLUSTERS, --n_clusters N_CLUSTERS

                        Number of clusters to split k-mers into. Valid options are "auto" or integer. Default is "auto".

  -peka PEKA_FILES [PEKA_FILES ...], --peka_files PEKA_FILES [PEKA_FILES ...]

                        A list of peka output files with extensions *mer_distribution_{region_name}.tsv, separated by spaces.

  -tl MIN_TOKEN_LENGTH, --min_token_length MIN_TOKEN_LENGTH

                        Minimal length of a substrings used for clustering. For k-mers with lengths greater than 5, setting this value to be greater than 1 can improve the results of clustering.

  -wl {True,False}, --weblogos {True,False}

                        Whether to plot weblogos for motif groups, True by default.

  -cons CONSENSUS_LENGTH, --consensus_length CONSENSUS_LENGTH

                        Length of consensus sequence to name k-mer groups. Automatically this length is determined as k-mer length - 1. Valid choices are "auto" or integer.

```