Find ORFs within a virus genome

It allows you to find orfs in fasta sequences of viral genomes.

If a reference is provided as genebank file, the script uses the min length of the orfs within the genebank file and determines automatically if the orfs should be overlapping or not.

This script relies on:

• python3
• pandas
• SeqIO

Which orfs can the script find:

Types:  
-----[M-------------*]-------- #complete
------M--[M---------*]-------- #complete_internal  
-----[M----------------------- #5_partial  
------M--[M------------------- #5_partial_internal  
[--------------------*]------- #3_partial  
[----------------------------] #5_3_partial  
------*]-------------[M------- #circular
------*]--------------M---[M-- #circular_internal

How the no overlap algorithm works:

no overlap algorithm:  
frame 1: -[M------*]-------[M--*]---------[M------
frame 2: -------[M------*]---------[M---*]--------  
frame 3: [M---*]-----[M----------*]----------[M---  

results: [M---*][M------*]-[M--*]-[M---*]-[M------  
frame:    3      2          1      2       1  

Installation and running:

# install the script:

git clone https://github.com/jonas-fuchs/viral_orf_finder
cd viral_orf_finder

# run the script:

python3 orf_finder.py infile.fasta > outfile.tabular

# optional arguments:

-r/--reference # reference genebank file
-m/--min-length # min length of the orfs to find
-i/--internal # True/False if script should search for internal orfs
-c/--circular # True/False if script should search for circular orfs
-p/--partial # True/False if script should search for partial orfs with no START and/or STOP
-n/--no-overlap # True/False if script should consider only orfs that do not overlap
-s/--strands # + and/or - (+ = positive strand, - = negative strand)

Side note:

The script has set the following codons:

start_codons = ["ATG"]
stop_codons = ["TAG", "TGA", "TAA"]

If you want to edit this you can do this directly by setting codons in the find_orfs function within the script.