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evatool-0.1.9
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مشاهده بیشترتوضیحات
Extracellular Vesicles small RNAs Abundance and quantification tool
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | evatool-0.1.9 |
| نام | evatool |
| نسخه کتابخانه | 0.1.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Dr. Xie and Dr. Liu |
| ایمیل نویسنده | xieguiyan@hust.eud.cn |
| آدرس صفحه اصلی | https://github.com/xieguiyan/EVAtool |
| آدرس اینترنتی | https://pypi.org/project/evatool/ |
| مجوز | MIT |
# **EVAtool**
---
### Quick start
If you would like to get start using EVAtool, please following the any of the follwing document.
* [**Quick start from PyPI**](https://pypi.org/project/evatool/)
* [**Quick start from Docker**](https://hub.docker.com/r/guobioinfolab/evatool)
### Introduction
EVAtool (EV analysis tool) is a state-of-the-art tool for quantification and abundance of small ncRNA-seq dataset in EVs. In EVAtool, we collected seven ncRNA types (miRNA, snoRNA, piRNA, snRNA, rRNA, tRNA and Y RNA) references as default to evaluate the abundence of each small ncRNA in EVs.
With current newest dependences (mainly bowtie2, samtool, fastq-dump, bedtools and trimmomatic-0.39.jar) and high-performance algorithm RDAA (Reads Dynamic Assignment Algorithm), the tool is perfectly capable of processing small RNA-seq data from small EVs (sEVs) or large EVs (lEVs). It is also capable of processing other RNA-seq data (such as long ncRNA data) with minor modifications to the command-line call. Finally, EVAtool visualized the main results and supports the online report.
EVAtool has been implemented in [Python >=3.5](#python), [Jupyter](#jupyter) and [HTML](#html).
### Table of Contents
* [System Requirements](#system-requirements)
* [Python](#python)
* [Installation with pip](#installation-with-pip)
* [Installation from source](#installation-from-source)
* [Quick Start by pip](#quick-start-by-pip)
* [Docker](#docker)
* [Installation](#installation)
* [Quick Start by docker](#quick-start-by-docker)
* [Advanced option](#advanced-option)
* [Directory tree](#directory-tree)
* [Help](#help)
### System Requirements
* Windows (>= 7), Mac OS X (>= 10.8) or Linux
* [Python >= 3.5](https://www.python.org/downloads/)
* [JDK 8](https://www.oracle.com/java/technologies/javase/javase8-archive-downloads.html)
All other software dependencies are installed automatically when installing EVAtool. Some softwares versions are as follows:
* samtools = 1.12 <br>
* bowtie2 = 2.4.2 <br>
* fastq-dump = 2.10.9 <br>
* trimmomatic-0.39.jar <br>
* bedtools = 2.30.0 <br>
### Python
#### Installation with `pip`
The Python version of EVAtool can be installed by running the following from a terminal:
pip install EVAtool
Installation of EVAtool and all dependencies should take no more than one minutes.
#### Installation from source
The Python version of PHATE can be installed from GitHub by running the following from a terminal:
git clone --recursive git@github.com:xieguiyan/EVAtool.git
cd EVAtool/
python setup.py install --user
#### Quick Start by pip
To begin, the human genome and seven types references needed to be download from http://bioinfo.life.hust.edu.cn/EVAtool/ref/refs.zip and unzip it into the working directory.
mkdir ~/evatool_work
cd ~/evatool_work
wget "http://bioinfo.life.hust.edu.cn/EVAtool/ref/refs.zip"
unzip refs.zip
If you have already prepared the data file (SRA, FASTQ or zipped FASTQ format) you can run EVAtool as follows (Here we use example.fastq.gz data as an example):
wget "http://bioinfo.life.hust.edu.cn/EVAtool/example/example.fastq.gz"
evatool \
-i example.fastq.gz
-o {directory for output or .}
EVAtool accepts the following data types: `example.sra`, `example.fastq` and `example.fastq.gz`.
### Docker
#### Installation
The docker image of evatool can be accessed by running the following from a terminal:
docker pull guobioinfolab/evatool
Then, prepare reference data and sequence data like the `pip` part:
mkdir ~/evatool_work
cd ~/evatool_work
wget "http://bioinfo.life.hust.edu.cn/EVAtool/ref/refs.zip"
unzip refs.zip
wget "http://bioinfo.life.hust.edu.cn/EVAtool/example/example.fastq.gz"
#### Quick Start by docker
Take the example.fastq.gz as example:
docker run -it -v $PWD:/work_path -w /work_path guobioinfolab/evatool -i example.fastq.gz -o .
### Advanced option
1. Custom ncRNA type(s)
- Based on existing reference sequences
- change the input parameter of ncRNA type list, the default ncRNAs are include 7 types: "miRNA" "rRNA" "tRNA" "piRNA" "snoRNA" "snRNA" "YRNA".
- Add other type reference sequences
- Three steps :
1. Add the ncRNA reference and index into refs;
```
mkdir [ncRNA name]
add the reference and index to the directory
```
2. Change the input parameter of ncRNA type list;
```
-n "miRNA" "rRNA" "tRNA"
```
3. Add the ncRNA name and reference directory in config file as following the existing ways.
```
"miRNA_index": "/refs/miRNA/hsa.hairpin.fa"
```
### Directory tree
```
├── bin
│ ├── bedtools
│ ├── bowtie2
│ ├── bowtie2-align-l
│ ├── bowtie2-align-l-debug
│ ├── bowtie2-align-s
│ ├── bowtie2-align-s-debug
│ ├── fastq-dump
│ ├── samtools
│ └── trimmomatic-0.39.jar
├── __init__.py
├── main.py
├── resource
│ ├── __init__.py
│ ├── logging.conf
│ ├── reference_config.json
│ ├── template_report.html
│ └── tool_config.json
└── utils
├── bam.py
├── config.py
├── fastq.py
├── __init__.py
├── logger.py
├── plot.py
├── report.py
├── sam.py
├── stat.py
└── tag.py
```
### Help
If you have any questions or require assistance using EVAtool, please contact us: xieguiyan@hust.edu.cn. More informations and usage could be found in the [**EVAtool web**](http://bioinfo.life.hust.edu.cn/EVAtool).
نیازمندی
| مقدار | نام |
|---|---|
| >=1.15 | numpy |
| - | pandas |
| >=0.9.0 | seaborn |
| - | jinja2 |
| - | pytest |
| - | pytest-cov |
| - | pytest-mock |
| - | pytest-xdist |
| - | tox |
| - | matplotlib |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.5 | Python |
نحوه نصب
نصب پکیج whl evatool-0.1.9:
pip install evatool-0.1.9.whl
نصب پکیج tar.gz evatool-0.1.9:
pip install evatool-0.1.9.tar.gz