PlottingOnGenome

Package to find and plot inserts alongside the genome or contigs.

BLAST is required. You can follow the instructions to download and install BLAST here.

Download

Click here to download the Windows executable.

If using this option, there is no need to follow any of the steps in the next section.

Install

Install with pip:

pip install git+https://git.embl.de/grp-zimmermann-kogadeeva/PlottingOnGenome.git

or with pipx (recommended):

pipx install git+https://git.embl.de/grp-zimmermann-kogadeeva/PlottingOnGenome.git

Whether using pip or pipx, python3 and git will need to be installed.

PyInstaler

Building exe in Windows using PyInstaller package:

pyinstaller -F -w -n plotting_on_genome -p .\plotting_on_genome\ --hidden-import Bio.SearchIO.BlastIO  .\pyinstaller_entry.py

Usage

This package can be used through GUI, CLI or through importing.

All interfaces require the same set of inputs:

• Search term - the search_term is required for downloading the genome of your interest from ncbi.
• Email - your email address is required to download genomes from NCBI.
• Forward suffix - suffix in your fasta files indicating forward sequences (default: _F)
• Reverse suffix - suffix in your fasta files indicating reverse sequences (default: _R)
• Filter threshold - threshold value for rejecting sequences with low coverage when determining whether a forward-reverse pair of sequences can be considered an insert
• Retmax - maximum number of records to be downloaded from NCBI
• Sequences file - location of your fasta file
• Output folder - location where to save all output files such as plots and the table of information on the inserts found

The package plots two types of plots: a circular graph of the whole genome or linear graphs of individual inserts along with the genes found in the same location on the genome.

Example