maylamolinari / prep-lasso

prep-LaSSO

Prepare input files for LaSSO - Lariat Sequence Site Origin software (https://github.com/dbitton/LaSSO.git)

Getting Started

Clone this repository into your local machine

git clone https://github.com/fernandalpcosta/prep-LaSSO.git

LaSSO software require two input files to make the database. The first one is a file with all the intron sequences. The second one is a file with some important information about those introns, the header file.

To understand all the fields that the header file needs to have, take a look inside LaSSO.R script at https://github.com/dbitton/LaSSO/blob/master/LaSSO.R

Here, I made a simple script to create the input header file for LaSSO, called getHeaderLaSSO.py

Prerequisites

• Python3 installed in your machine
• Gff3 file with just intron information
• Gff3 file with just exon information

Installing

No installation is required, the script is ready to use (executable).

python3 getHeaderLaSSO.py

Usage

Once you have ran the getHeaderLaSSO.py script, it will prompt for two files, the gff3 of your introns and gff3 of your exons.

Important: both files has to be from the same source, compatible in ids. On other words, from the same genome version.

Authors

• Fernanda Luz P Costa - Initial work - fernandalpcosta

Contributors

• Mayla Daiane Correa Molinari

License

Open-source