orfipy
Project description
Introduction
orfipy is a python package to extract ORFs in extremely fast and flexible manner.
Installation
Install from source
git clone https://github.com/urmi-21/orfipy.git
cd orfipy
pip install .
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
Project details
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Source Distribution
orfipy-0.0.1.tar.gz
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