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

pip install orfipy

Or install via conda

conda install -c bioconda orfipy

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

Details of orfipy algorithm are in the preprint and SI. Please go through the SI if you are interested to know differences between orfipy and other ORF finder tools and how to set orfipy parameters to match the output of other tools.

Below are some usage examples for orfipy

To see full list of options use the command:

orfipy -h

orfipy currently supports sequences in only Fasta format. If you want to directly work with compressed Fasta files, compression format must be bgzip. To use Fastq files, you will need to first convert them to Fasta.

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

Note: Users can also provide their own translation table, as a .json file, to orfipy using --table option. Example of json file containing a valid translation table is here

See available codon tables

orfipy --show-table

Extract ORFs BED file

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

Extract ORFs 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 ORFs peptide sequences using default translation table

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

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