seq-here 0.1.0

A fast tool for bio-sequence file processing.
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

![seq-here](.github/avatar.png)

---

[![Version](https://img.shields.io/badge/version-0.1.0-yellow.svg)]()
[![GitHub](https://img.shields.io/badge/github-bio--here%2Fseq--here-blue.svg)](https://github.com/bio-here/seq-here)
[![Build Status](https://travis-ci.org/bio-here/seq-here.svg?branch=master)](https://travis-ci.org/bio-here/seq-here)
[![Crates.io](https://img.shields.io/crates/v/seq-here.svg)](https://crates.io/crates/seq-here)
[![Documentation](https://docs.rs/seq-here/badge.svg)](https://docs.rs/seq-here)
[![License](https://img.shields.io/crates/l/MIT.svg)]()

## Introduction

Seq-here is a fast tool for bio-sequence file processing.

## Installation

You can install `seq-here` using `cargo`:

```shell
cargo install seq-here
```

or you can build it from source:

```shell
git clone git@github.com:bio-here/seq-here.git
cd seq-here
cargo build --release
cp target/release/seq-here /usr/local/bin

seq-here --version
```

## Lib Crate

You can also use `seq-here` as a library crate in your project, 
by adding the following to your `Cargo.toml`:

```toml
[dependencies]
seq-here = "0.1.0"
```


## Usage
To see detailed usage information, you can run:

```shell
seq-here --help
```


- **Info**: Get basic information about the input sequence file(s).

```shell
# Fasta file information
seq-here info fa you_files.fasta,your_files2.fasta

# Fastq file information
seq-here info fq your_files.fastq

# Gff/Gtf file information, Gff2 not supported yet
seq-here info gff your_files.gff

# -o, --output: output method, default is println
# 3 options: println, file, csv
# The file will be put in the current directory
seq-here info fa your_files.fasta -o file

# input a directory to get all files information below the directory
seq-here info fa your_dir
```

- **Process**: Convert or process incoming sequence file(s).

```shell
# Combine files
seq-here process combine files_folder
seq-here porcess combine file1,file2,file3

# -o, --output <OutputFile>
#         Output file name, if value is a directory, it would use default file_name in the directory.


seq-here process combine files_folder -o ./output/all.txt
```

- **Extract**: Extract specified sequence segment or file data.

```shell
# Extract a sequence segment by id
seq-here extract segment input.fasta --file sequence_id.txt
seq-here extract segment input.fasta --str GhID00000001

# Extract a specific portion of a sequence by position (0-based coordinates)
seq-here extract segment input.fasta --str GhID00000001 --start 100 --end 200
seq-here extract segment input.fasta --file ids.txt --start 50 --end 150

# Extract sequences by given annotation file
seq-here extract explain --seq input.fasta --gff input.anno.gff -o output_path.fasta

# Extract only specific feature types from annotations
seq-here extract explain --seq input.fasta --gff input.anno.gff --type CDS,gene,mRNA -o output_path
```


## Contributing

Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.


## License

This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.