Skip to main content


Project description

Build Status


orfipy is a python package to extract ORFs in extremely fast and flexible manner.


Install from source

git clone
cd orfipy
pip install .


Extract ORF sequences and write ORF sequences in orfs.fa file

orfipy input.fasta --dna orfs.fa --min 10 --max 10000 --procs 4 --table 1 --outdir orfs_out

Use standard codon table but use only ATG as start codon

orfipy input.fasta --dna orfs.fa --start ATG

Extract ORF BED file

orfipy input.fasta --bed orfs.bed --min 50 --procs 4
orfipy input.fasta --min 50 --procs 4 > orfs.bed 

Extract ORF BED12 file

Note: Add --include-stop for orfipy output to be consistent with Transdecoder.Predict output .bed file

orfipy testseq.fa --min 100 --bed12 of.bed --partial-5 --partial-3 --include-stop

Extract peptides

orfipy input.fasta --pep orfs_peptides.fa --min 50 --procs 4

See available codon tables

orfipy --show-table

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

orfipy-0.0.1.tar.gz (89.8 kB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page