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https://github.com/ebedthan/hyperex
Hypervariable region primer-based extractor for 16S rRNA and other SSU/LSU sequences.
https://github.com/ebedthan/hyperex
16s-rrna bioinformatics rust-lang
Last synced: 16 days ago
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Hypervariable region primer-based extractor for 16S rRNA and other SSU/LSU sequences.
- Host: GitHub
- URL: https://github.com/ebedthan/hyperex
- Owner: Ebedthan
- License: mit
- Created: 2021-08-02T02:24:23.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-04-02T15:00:32.000Z (8 months ago)
- Last Synced: 2024-11-02T12:06:59.262Z (16 days ago)
- Topics: 16s-rrna, bioinformatics, rust-lang
- Language: Rust
- Homepage:
- Size: 403 KB
- Stars: 9
- Watchers: 3
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
## About
HyperEx (pronounced "Hyper Ex" for Hypervariable region Extractor) is a tool that extracts 16S ribosomal RNA (rRNA) hypervariable region based on a set of primers. By default when no option is specified, hyperex extracts all hypervariable region from the supplied sequences assuming 16S rRNA sequences. To do this it has a set of built-in primer sequences which are universal 16S primers sequences.
Nevertheless, the user can choose to specify the wanted region by specifying the `--region` option or by providing the primer sequences using `--forward-primer` and `--reverse-primer`. The `--region` option takes only the region names like "v1v2" or "v4v5" while the `--forward-primer` and `--reverse-primer` takes only the sequences which can contains IUPAC ambiguities.
For more than one needed region, one can use multiple time the `--region`, `--forward-primer`, `reverse-primer` options to specify the wanted region. Theses option takes only one argument, but can be repeat multiple time (see Examples below).
For more praticability, the user can also provide a supplied file containing primer sequences to extract the wanted region using the `--region` option. The primer sequences file should be a no header comma separated value file like:
```
FORWARD_PRIMER_1,REVERSE_PRIMER_1
FORWARD_PRIMER_2,REVERSE_PRIMER_2
...
```
Moreover, one can allow a number of mismatch in the primer sequence using the `--mismatch` option.
The outputs are a fasta file containing the extracted regions and a GFF3 file indicating the extracted regions positions.
## Installation
### Using prebuilt binaries
Please see the [releases page](https://github.com/Ebedthan/hyperex/releases) for prebuilt binaries for major operating system
### From crates.io
If you already have a functional rust installation you can easily do:
```
cargo install hyperex
```
And that's all!
### From source
```
git clone https://github.com/Ebedthan/hyperex.git
cd hyperex
cargo build --release
cargo test
# To install hyperex in current directory
cargo install --path .
```
And you are good to go!
## How to run hyperex ?
### By default with no options
```
# reading data from a specified file
hyperex file.fa
# reading data from standard input
cat file.fa | hyperex
```
### Using built-in 16S primer names
```
# reading data from a specified file
hyperex -f 27F -r 337R file.fa.gz
# reading data from standard input
zcat file.fa.gz | hyperex -f 27F -r 337R
```
### Using built-in 16S region names
```
# reading data from a specified file
hyperex --region v3v4 file.fa.xz
# reading data from standard input
xzcat file.fa.xz | hyperex --region v3v4
```
### Using custom primer sequences
```
# reading data from a specified file
hyperex -p prefix --forward-primer ATCG --reverse-primer TYAATG file.fa.bz2
# reading data from standard input
bzcat file.fa.bz2 | hyperex -p prefix --forward-primer ATCG --reverse-primer TYAATG
```
### Using custom list of primers: primers.txt
```
hyperex --region primers.txt file.fa
```
### Using multiple primers
```
hyperex --region v1v2 --region v3v4 file.fa
hyperex -f ATC -f YGA -r GGCC -r TTRC file.fa
```
## Usage
### Command line arguments
```
hyperex [FLAGS] [OPTIONS]
```
#### Flags:
```
--force Force output overwritting
-q, --quiet Decreases program verbosity
-h, --help Prints help information
-V, --version Prints version information
```
#### Options:
```
-f, --forward-primer ... Specifies forward primer sequence. Can be a sequence with degenerate bases
-r, --reverse-primer ... Specifies reverse primer sequence. Can be a sequence with degenerate bases
--region ... Specifies a hypervariable region to extract
-m, --mismatch Specifies number of allowed mismatch [default: 0]
-p, --prefix Specifies the prefix for the output files [default: hyperex_out]
```
#### Args:
```
Input fasta file. Can be gzip'd, xz'd or bzip'd
```
## Requirements
### Mandatory
- [Rust](https://rust-lang.org) in stable channel
### Optional
- libgz for gz file support
- liblzma for xz file support
- libbzip2 for bzip2 file support
## Note
hyperex use colored output in help, nevertheless hyperex honors [NO_COLORS](https://no-color.org/) environment variable.
## Bugs
Submit problems or requests to the [Issue Tracker](https://github.com/Ebedthan/hyperex/issues).