packbed 0.0.7

pack a .bed into overlapping components
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117

<p align="center">
  <h1 align="center">
    packbed
  </h1>

  <p align="center">
    <a href="https://img.shields.io/badge/version-0.0.1dev-green" target="_blank">
      <img alt="Version Badge" src="https://img.shields.io/badge/version-0.0.1-green">
    </a>
    <a href="https://crates.io/crates/packbed" target="_blank">
      <img alt="Crates.io Version" src="https://img.shields.io/crates/v/packbed">
    </a>
    <a href="https://github.com/alejandrogzi/packbed" target="_blank">
      <img alt="GitHub License" src="https://img.shields.io/github/license/alejandrogzi/packbed?color=blue">
    </a>
    <a href="https://crates.io/crates/packbed" target="_blank">
      <img alt="Crates.io Total Downloads" src="https://img.shields.io/crates/d/packbed">
    </a>
  </p>


  <p align="center">
    pack a .bed into overlapping components
  </p>

</p>

<p align="center">
    <img width=700 align="center" src="./.github/assets/img.png">
</p>


## Features
- pack any number of .bed files into overlapping components through a binary, Rust library or Python module
- write a unique overlapping-component-colorized bed file out of any number of .bed files through a binary, Rust library or Python module
- split components into separate .bed files through a binary, Rust library or Python module
- write serialized components to a binary file through a binary and Rust library
- read serialized components from a binary file through a Rust library or Python module
- write specific components each to a different .bed file through a Rust library or Python module

> What's new on packbed v0.0.6!
>
> - Fixes lost overlapping components because of sorting step
> - Adds --overlap_exon flag to overlap only exon regions (no UTR-aware)

## Usage
### Binary
``` bash
Usage: packbed [OPTIONS] --bed <PATHS>... --output <PATH>

Arguments:
    -b, --bed <PATHS>...     Paths to BED12 files delimited by comma
    -o, --output <PATH>      Path to output BED12 file [not required if -c flag is set]

Options:
    -t, --threads <THREADS>  Number of threads [default: 8]
    --type <TYPE>   Type of output [default: bed] [possible values: bin, comp, bed]
    --overlap_cds   Flag to overlap only cds regions
    --overlap_exon  Flag to overlap only exon regions
    -s, --subdirs   Flag to split components into separate BED files in subdirectories
    --colorize      Flag to colorize components in output BED(s) file
    -h, --help      Print help
    --version:      Print version
```

> [!TIP]
> If you want to get components in separate .bed files use:
> ```bash
> packbed -b path/to/b1.bed,path/to/b2.bed -o path/to/output --type comp
> ```
> in case you want to send each component to a different subdirectory (good to parallelize processes):
> ```bash
> packbed -b path/to/b1.bed,path/to/b2.bed -o path/to/output --type comp -s
> ```
> if you want to colorize the components but send them all to just 1.bed file [default]:
> ```bash
> packbed -b path/to/b1.bed,path/to/b2.bed -o path/to/output --colorize
> ```

### Library
``` rust
use packbed::packbed;

fn main() {

    let bed1 = PathBuf::new("/path/to/b1.bed");
    let bed2 = PathBuf::new("/path/to/b2.bed");
    let beds = vec![bed1, bed2];

    let overlap_cds = true;
    let overlap_exon = false;
    let colorize = true;

    let comps: HashMap<String, Vec<Vec<Arc<GenePred>>>> = packbed(
                        beds,
                        overlap_cds,
                        overlap_exon,
                        colorize)
                        .unwrap();
}
```
### Python
build the port to install it as a pkg:
```bash
git clone https://github.com/alejandrogzi/packbed.git && cd packbed/py-packbed
hatch shell
maturin develop --release
```
use it:
``` python
from packbed import pack

beds = ["path/to/bed1.bed", "path/to/bed2.bed"]
comps = pack(beds)
```

### crate: [https://crates.io/crates/packbed](https://crates.io/crates/packbed)