Jcvi

Introduction

Jcvi is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

For more information, please check:

Home page: https://github.com/tanghaibao/jcvi

Versions

• 1.2.7

• 1.3.1

Commands

• python

• python3

Module

You can load the modules by:

module load biocontainers
module load jcvi

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run jcvi on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=jcvi
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers jcvi

python -m jcvi.formats.fasta format Vvinifera_145_Genoscope.12X.cds.fa.gz grape.cds
python -m jcvi.formats.fasta format Ppersica_298_v2.1.cds.fa.gz peach.cds
python -m jcvi.formats.gff bed --type=mRNA --key=Name --primary_only Vvinifera_145_Genoscope.12X.gene.gff3.gz -o grape.bed
python -m jcvi.compara.catalog ortholog grape peach --no_strip_names
python -m jcvi.graphics.dotplot grape.peach.anchors
rm grape.peach.last.filtered
python -m jcvi.compara.catalog ortholog grape peach --cscore=.99 --no_strip_names
python -m jcvi.graphics.dotplot grape.peach.anchors
python -m jcvi.compara.synteny depth --histogram grape.peach.anchors
python -m jcvi.graphics.grabseeds seeds test-data/test.JPG