https://github.com/andreaguarracino/motifence
https://github.com/andreaguarracino/motifence
Last synced: 2 months ago
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- Host: GitHub
- URL: https://github.com/andreaguarracino/motifence
- Owner: AndreaGuarracino
- License: mit
- Created: 2024-04-08T15:06:56.000Z (about 1 year ago)
- Default Branch: master
- Last Pushed: 2024-08-12T09:11:38.000Z (10 months ago)
- Last Synced: 2025-01-24T16:38:08.354Z (4 months ago)
- Language: Rust
- Size: 7.81 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Motifence
`motifence` is a command-line tool designed to find specified motifs in a FASTA file and output them in BED format with additional details.
## Features
- Supports both uncompressed and gzipped FASTA files.
- Allows specifying motifs via command-line arguments or a file.
- Outputs results in BED format, including the matched sequence.
## Installation
To install `motifence`, you need to have Rust and Cargo installed.
Clone the repository:
```shell
git clone https://github.com/yourusername/motifence.git
cd motifence
```
Build the project:
```shell
cargo build --release
```
The executable will be located in `target/release/`. You can add this directory to your `PATH` or move the executable to a directory that is already in your `PATH`.
## Usage
Search for a single motif and write results to stdout:
```shell
motifence --fasta sequences.fasta --motif ATGC
```
Search for motifs listed in a file and write results to a BED file:
```shell
motifence --fasta sequences.fasta --motif_file motifs.txt --bed results.bed
```
Search for a single motif in a gzipped FASTA file and write results to stdout:
```shell
motifence --fasta sequences.fasta.gz --motif ATGC
```
## Output Format
The output is in BED format with the following columns:
- Chromosome/Sequence ID
- Start position (0-based)
- End position (1-based)
- Motif
- Dot (.)
- Strand (+ or -)
Matched sequence
Example output:
```shell
chr1 100 104 ATGC . + ATGC
chr2 200 204 ATGC . - GCAT
```