Extract gene TSS site form gencode/ensembl/gencode database GTF file and export bed format file.

Related tags

Web CrawlingGetTss
Overview

GetTss python Package

extract gene TSS site form gencode/ensembl/gencode database GTF file and export bed format file.

Install

$ pip install GetTss

Usage

help infomation:

$ GetTss -h
usage: GetTss --database ucsc --gtffile hg19.ncbiRefSeq.gtf --tssfile testTSS.bed

Get gene TSS site and export bed format from GTF annotation file.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -d {ucsc,ensembl,gencode}, --database {ucsc,ensembl,gencode}
                        which annotation database you choose. (default="ensembl")
  -g GTFFILE, --gtffile GTFFILE
                        input your GTF file. (ucsc/ensembl/gencode)
  -t TSSFILE, --tssfile TSSFILE
                        output your TSS file. (test-TSS.bed)

Thank your for your support, if you have any questions or suggestions please contact me: [email protected].

for ucsc gtf file:

$ GetTss -d ucsc -g hg19.ncbiRefSeq.gtf -t ucsc-TSS.bed
Your job is starting, please wait!
You GTF file have: 104178 transcripts.
 
Your task has down!

$ head -n 3 ucsc-TSS.bed
chrMT   16023   16024   TRNP    .       -
chrMT   15887   15888   TRNT    .       +
chrMT   14746   14747   CYTB    .       +

for gencode/ensembl gtf file:

$ GetTss -d gencode -g gencode.v19.annotation.gtf -t test-TSS.bed
Your job is starting, please wait!
You GTF file have: 57820 genes.

Your task has down!

$ head -n 3 test-TSS.bed
chr1    11868   11869   ENSG00000223972.4       .       +
chr1    29806   29807   ENSG00000227232.4       .       -
chr1    29553   29554   ENSG00000243485.2       .       +

plot peaks density around TSS

compute matrix:

$ computeMatrix reference-point -S normal.bw treat.bw \
                -R myTSS.bed \
                --referencePoint center \
                -a 3000 -b 3000 -p 25 \
                -out matrix.tab.gz

plot Profile:

$ plotProfile -m matrix.tab.gz \
              -out profile.pdf \
              --perGroup \
              --plotTitle 'test profile'
Owner
laojunjun
路漫漫其修远兮 吾将上下而求索
laojunjun
Automatically scrapes all menu items from the Taco Bell website

Automatically scrapes all menu items from the Taco Bell website. Returns as PANDAS dataframe.

Sasha 2 Jan 15, 2022
Instagram profile scrapper with python

IG Profile Scrapper Instagram profile Scrapper Just type the username, and boo! :D Instalation clone this repo to your computer git clone https://gith

its Galih 6 Nov 07, 2022
A Python Covid-19 cases tracker that scrapes data off the web and presents the number of Cases, Recovered Cases, and Deaths that occurred because of the pandemic.

A Python Covid-19 cases tracker that scrapes data off the web and presents the number of Cases, Recovered Cases, and Deaths that occurred because of the pandemic.

Alex Papadopoulos 1 Nov 13, 2021
a small library for extracting rich content from urls

A small library for extracting rich content from urls. what does it do? micawber supplies a few methods for retrieving rich metadata about a variety o

Charles Leifer 588 Dec 27, 2022
New World Market Scraper

Bean Seller A New Worlds market scraper. Deployment This must be installed on Windows as it uses the Windows api to do its stuff Install Prerequisites

4 Sep 21, 2022
FilmMikirAPI - A simple rest-api which is used for scrapping on the Kincir website using the Python and Flask package

FilmMikirAPI - A simple rest-api which is used for scrapping on the Kincir website using the Python and Flask package

UserGhost411 1 Nov 17, 2022
An automated, headless YouTube Watcher and Scraper

Searches YouTube, queries recommended videos and watches them. All fully automated and anonymised through the Tor network. The project consists of two independently usable components, the YouTube aut

44 Oct 18, 2022
抖音批量下载用户所有无水印视频

Douyincrawler 抖音批量下载用户所有无水印视频 Run 安装python3, 安装依赖

28 Dec 08, 2022
An application that on a given url, crowls a web page and gets all words, sorts and counts them.

Web-Scrapping-1 An application that on a given url, crowls a web page and gets all words, sorts and counts them. Installation Using the package manage

adriano atambo 1 Jan 16, 2022
A high-level distributed crawling framework.

Cola: high-level distributed crawling framework Overview Cola is a high-level distributed crawling framework, used to crawl pages and extract structur

Xuye (Chris) Qin 1.5k Jan 04, 2023
Web scrapping tool written in python3, using regex, to get CVEs, Source and URLs.

searchcve Web scrapping tool written in python3, using regex, to get CVEs, Source and URLs. Generates a CSV file in the current directory. Uses the NI

32 Oct 10, 2022
A python script to extract answers to any question on Quora (Quora+ included)

quora-plus-bypass A python script to extract answers to any question on Quora (Quora+ included) Requirements Python 3.x

Nitin Narayanan 10 Aug 18, 2022
Scrape puzzle scrambles from csTimer.net

Scroodle Selenium script to scrape scrambles from csTimer.net csTimer runs locally in your browser, so this doesn't strain the servers any more than i

Jason Nguyen 1 Oct 29, 2021
京东云无线宝积分推送,支持查看多设备积分使用情况

JDRouterPush 项目简介 本项目调用京东云无线宝API,可每天定时推送积分收益情况,帮助你更好的观察主要信息 更新日志 2021-03-02: 查询绑定的京东账户 通知排版优化 脚本检测更新 支持Server酱Turbo版 2021-02-25: 实现多设备查询 查询今

雷疯 199 Dec 12, 2022
A webdriver-based script for reserving Tsinghua badminton courts.

AutoReserve A webdriver-based script for reserving badminton courts. 使用说明 下载 chromedriver 选择当前Chrome对应版本 安装 selenium pip install selenium 更改场次、金额信息dat

Payne Zhang 4 Nov 09, 2021
Dex-scrapper - Hobby project for scrapping dex data on VeChain

Folders /zumo_abis # abi extracted from zumo repo /zumo_pools # runtime e

3 Jan 20, 2022
Web Scraping COVID 19 Meta Portal with Python

Web-Scraping-COVID-19-Meta-Portal-with-Python - Requests API and Beautiful Soup to scrape real-time COVID statistics from worldometer website and perform data cleaning and visual analysis in Jupyter

Aarif Munwar Jahan 1 Jan 04, 2022
此脚本为 python 脚本,实现原理为利用 selenium 定位相关元素,再配合点击事件完成浏览器的自动化.

此脚本为 python 脚本,实现原理为利用 selenium 定位相关元素,再配合点击事件完成浏览器的自动化.

N0el4kLs 5 Nov 19, 2021
Open Crawl Vietnamese Text

Open Crawl Vietnamese Text This repo contains crawled Vietnamese text from multiple sources. This list of a topic-centric public data sources in high

QAI Research 4 Jan 05, 2022
Web scrapper para cotizar articulos

WebScrapper Este web scrapper esta desarrollado en python 3.10.0 para buscar en la pagina de cyber puerta articulos dentro del catalogo. El programa t

Jordan Gaona 1 Oct 27, 2021