placecare 1.1.0

A toolkit to quickly search for cis-acting regulatory elements using the PLACE database
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

[![Version](https://img.shields.io/badge/version-1.1.0-green.svg?style=for-the-badge)]()
[![GitHub](https://img.shields.io/badge/github-bio--here%2Fplacecare-blue.svg?style=for-the-badge)](https://github.com/bio-here/placecare)
[![Crates.io](https://img.shields.io/crates/v/placecare?style=for-the-badge)](https://crates.io/crates/placecare)
[![Documentation](https://img.shields.io/docsrs/placecare/latest?style=for-the-badge)](https://docs.rs/placecare)
[![License](https://img.shields.io/crates/l/MIT.svg?style=for-the-badge)]()
[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/bio-here/placecare)

Read documentation in other languages:
- [中文](README-zh.md)

# PLACE-CARE

placecare is a tool for predicting cis-acting elements based on string search algorithms using the PLACE database.

With placecare, you can:

1. Upload sequence files to search for cis-acting elements.

2. Quickly retrieve relevant information through PLACE database's id and ac
(Data comes from the place.seq file provided by the official PLACE website)


# Installation

If your computer has the Rust toolchain, you can install our command-line program with the following command:

```shell
cargo install placecare
```

If you don't have the Rust toolchain installed, you can also download our compiled binary files directly from GitHub's Release:
- [Release](https://bio-here.github.io/placecare/release)


If you want to use our library, you just need to:
```shell
cargo add placecare
```

# Usage

See more on [bio-here/placecare](https://bio-here.github.io/placecare)

This section introduces how to use our library.
The core functionality of placehere is written in the `place_search` module, I/O operations are written in the `io` module,
and the `place_desc` module describes the PLACE data.

## Search Elements

We provide multiple ways to input sequences, as shown below:
```rust
use placehere::io::RecordDesc;

let input = vec![RecordDesc::new("Gh_01", "TTATAGACTCGATGGCCGCGCGG")];
let input = RecordDesc::from_file("./input.fasta");
let input = RecordDesc::from_string("\
>Gh_01
ATATCCGGATGGCATGCTGATC
");
let input = RecordDesc::from_records(bio::io::fasta::Reader::new("./input.fasta"));

let mut f = File::open("input.txt").unwrap();
let input = RecordDesc::from_reader(f);
```

Then we can search:
```rust
use placecare::place_search::Search;

// Search for a single element
let result = Search::search_element(input).unwrap();

// Search for multiple elements
let result = Search::search_elements(input).unwrap();
```

You can view the definitions in the `place_desc` module to understand the output information.

## Query Element Information

We can use the following methods to query element information in the PLACE database.
```rust
use placecare::search::Search;

The function will return a vector of Option<SeqDesc>
// for which is a result of the input sequence.
let e1: Vec<Option<SeqDesc>> = query_elements_by_id(&vec!["TATABOX1", "TATABOX2"]);
let e2: Vec<Option<SeqDesc>> = query_elements_by_ac(&vec!["S000023", "S000260"]);
```

# Tips

## IUPAC Ambiguous Bases
The PLACE database uses IUPAC ambiguous base symbols ([Wikipedia](https://en.wikipedia.org/wiki/Nucleic_acid_notation)) to represent multiple possible bases.

# License
placecare is an open-source project under the MIT license. You are free to use, modify, and distribute this software, but please retain the original author's copyright notice and license information.