jcvi
Link to section 'Introduction' of 'jcvi' Introduction
Jcvi is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
Home page: https://github.com/tanghaibao/jcvi
Link to section 'Versions' of 'jcvi' Versions
- 1.2.7
- 1.3.1
Link to section 'Commands' of 'jcvi' Commands
- python
- python3
Link to section 'Module' of 'jcvi' Module
You can load the modules by:
module load biocontainers
module load jcvi
Link to section 'Example job' of 'jcvi' Example job
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