Replace sequence_IDs in gff3 based on given genome.fasta

Last update: Nov 12, 2021

Related tags

Overview

gff-rename

Replace the sequence IDs in a gff3 file with a set of provided sequence IDs from a genom.fasta. This is useful when a gff3 file is retrieved from Ensembl whereas the genome.fasta is from NCBI as the gff3 file will use Chromosome IDs whereas the genome.fasta will use GenBank sequence IDs. Running this script will convert the sequence IDs in the gff3 file to match those from the genome.

Install


git clone https://github.com/tolkit/gff-rename
cd gff-rename
chmod +x gff-rename

Usage

gff-rename

gff3-rename
Charlotte Wright 
   
     
Convert_gff3_IDs.py [-h] [--genome GENOME] [--gff3 GFF3] [--prefix PREFIX]

This converts sequence_IDs from a gff3 to sequence_IDs from a given genome fasta file

optional arguments:
  -h, --help       show this help message and exit
  --genome GENOME  This is the genome fasta
  --gff3 GFF3      This is the gff3 file
  --prefix PREFIX  This is the prefix for the output file

Owner

tolkit

Tree of Life Kit

GitHub Repository

Install and manage Proton-GE and Luxtorpeda for Steam and Wine-GE for Lutris with this graphical user interface. Based on AUNaseef's ProtonUp, made with Python 3 and Qt 6.

ProtonUp-Qt Qt-based graphical user interface to install and manage Proton-GE installations for Steam and Wine-GE installations for Lutris. Based on A

638 Jan 02, 2023

Telegram Voice-Chat Bot

Telegram Voice-Chat Bot [PyTGCalls] ⇝ Requirements ⇜ Account requirements A Telegram account to use as the music bot, You cannot use regular bot accou

1 Dec 03, 2021

The best Discord bot, created for r/Jailbreak

Bloo Setup instructions These instructions assume you are on macOS or Linux. Windows users, good luck. With Docker (recommended!) You will need the fo

33 Dec 16, 2022

Home Assistant Hilo Integration via HACS

BETA This is a beta release. There will be some bugs, issues, etc. Please bear with us and open issues in the repo. Hilo Hilo integration for Home Ass

66 Dec 23, 2022

A simple python discord bot with commands for moderation and utility.

Discord Bot A simple python discord bot with commands for moderation, utility and fun. Moderation $kick user reason - Kick a user from the server

3 Feb 06, 2022

A Python implementation of a discord bot that acts as a server scanner similar to Copenheimer.

Bad Copenheimer A Python impelentation of a discord bot that acts as a server scanner. This is a discord bot that will scan ip adresses to see if they

69 Dec 16, 2022

A Python package that can be used to download post and comment data from Reddit.

Reddit Data Collector Reddit Data Collector is a Python package that allows a user to collect post and comment data from Reddit. It is built on top of

3 Jul 26, 2022

Bot made by BLACKSTORM[BM] Contact Us - t.me/BLACKSTORM18

ᴡʜᴀᴛ ɪs ᴊᴀʀᴠɪs sᴇᴄᴜʀɪᴛʏ ʙᴏᴛ ᴊᴀʀᴠɪs ʙᴏᴛ ɪs ᴛᴇʟᴇɢʀᴀᴍ ɢʀᴏᴜᴘ ᴍᴀɴᴀɢᴇʀ ʙᴏᴛ ᴡɪᴛʜ ᴍᴀɴʏ ғᴇᴀᴛᴜʀᴇs. ᴛʜɪs ʙᴏᴛ ʜᴇʟᴘs ʏᴏᴜ ᴛᴏ ᴍᴀɴᴀɢᴇ ʏᴏᴜʀ ɢʀᴏᴜᴘs ᴇᴀsɪʟʏ. ᴏʀɪɢɪɴᴀʟʟʏ ᴀ

1 Dec 11, 2021

A telegram bot to download mega.nz links. (made with pyrogram).

Mega Link Downloader Bot This is a telegram bot to download mega.nz links and return them as files/videos - Made by a 100% noob! (When I mean noob I r

171 Dec 27, 2022

Visionary-OS: open source discord bot

Visionary-OS Our Visionary open source discord bot. Our goal is to create a discord bot, which is hosted by us, but every member of our community can

8 Jan 27, 2022

Autofill HZDR Zeitman entries

Zeitman_autofill Filling out Zeitman is boring. This script might make some of the pain go away. Requirements The selenium package and Chrome webdrive

8 Mar 14, 2022

An unofficial Python wrapper for the 'Binance exchange REST API'

Welcome to binex_f v0.1.0 many interfaces are heavily used by myself in product environment, the websocket is reliable (re)connected. Latest version:

2 Jan 05, 2022

The Python client library for the Tuneup Technology App.

Tuneup Technology App Python Client Library The Python client library for the Tuneup Technology App. This library allows you to interact with the cust

0 Jun 29, 2022

Utilizing the freqtrade high-frequency cryptocurrency trading framework to build and optimize trading strategies. The bot runs nonstop on a Rasberry Pi.

Freqtrade Strategy Repository Please test all scripts and dry run them before using them in live mode Contact me on discord if you have any questions!

90 Jan 01, 2023