orfipy 0.0.2

orfipy

Introduction

orfipy is a tool written in python/cython to extract ORFs in extremely fast and flexible manner. Please read the preprint here

Installation

Install latest stable version

pip install orfipy

Install development version from source

git clone https://github.com/urmi-21/orfipy.git
cd orfipy
pip install .

or use pip

pip install git+git://github.com/urmi-21/orfipy.git

Examples

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
or
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

Comparison with getorf and OrfM

Comparison of orfipy features and performance with getorf and OrfM. For details see preprint and SI