Genome Management Package

This tool is copyright 2016 by Nattawet Sriwichai, King Mongkut's University Technology Thonburi (Bioinformatics and Systems Biology Program), Thailand. All rights reserved. See the licence text below.

Installation

Install from PyPI

pip install genomemanagement

Install from GitHub

pip install git+https://github.com/evolu-tion/GenomeManagement.git

Install from Source (Standard)

git clone https://github.com/evolu-tion/GenomeManagement.git
cd GenomeManagement
pip install .

Install for Development (Editable)

pip install -e .

Usage: Promoter of genes retrieving

Then run python script by used command line on windows or unix:

promoter-retrieve \
	--output <output_file.fa> \
	--output_format <fasta/gff> \
	--genome <genome.fa> \
	--gff <genome.gff> \
	--type <TLS/TSS> \
	--upstream <bp> \
	--downstream <bp> \
	--all_gene <Y/N> \
	--selected_gene_list <gene_list.txt, is optional if all_gene is N> \
	--remove_n_gap <Y/N> \
	--min_length <default is 100 bp>

Usage: Get protein or gene sequences from genome

proteins-retrieve \
	--input <input_fasta_file> \
	--list_of_interest <list_of_protein_id.txt> \
	--output <output_file.fa>

Usage: PlantPAN3

plantpan3

Usage: Get genome statistic

get-genome-statistic \
	--genome <genome.fa>

License

This project is licensed under the MIT License - see the LICENSE file for details.