Syntgeny
Tool to detect if the gene order is conserved over a set of taxa
Installation
Syntegny requires the targeted ortholog search tool fDOG. For installation and setup of fDOG, you can just look on the fDOG GitHub page.
Usage
Syntgeny requires the same data structure as described in the fDOG manual.
python3 syntgeny.py --seed 'maker-scaffold8-snap-gene-67.113' --jobName <Name> --refSpec <reference Species> --gff .<gff_folder> --neighbours <number neighbours upstream and downstream> --out <folder> --searchpath <searchTaxa_dir> --corepath <coreTaxa_dir> --annopath <annotation_dir>
Example Output
Extracting neighbours of seed gene maker-scaffold8-snap-gene-67.113
Starting fDOG for seed gene and identified neighbours
fdogs.run --seqFolder ./tmp/seeds/ --jobName test --refspec DIPRO@73405@230629 --outpath . --corepath ../data/coreTaxa_dir --searchpath ../data/searchTaxa_dir --annopath ../data/annotation_dir
100%|████████████████████████████████████████████████████████████████████████████████████| 5/5 [04:09<00:00, 49.91s/it]
fDOG finished. Parsing fDOG output and extracting ortholog locations
Creating output table
Run time -265.59861493110657`sec
Parameters:
usage: syntgeny.py [-h] [--version] --seed SEED --refSpec REFSPEC --neighbours NEIGHBOURS --gff GFF --jobName JOBNAME [--fasta FASTA] [--searchTaxa SEARCHTAXA] [--out OUT]
[--searchpath SEARCHPATH] [--corepath COREPATH] [--annopath ANNOPATH]
You are running Syntgeny version 0.0.1.
options:
-h, --help show this help message and exit
--version show program's version number and exit
Required arguments:
--seed SEED Seed gene name
--refSpec REFSPEC Reference taxon
--neighbours NEIGHBOURS
Number of neighbouring genes up and downstream that should be checked
--gff GFF Path to gff file of reference species
--jobName JOBNAME Job name
Optional arguments:
--fasta FASTA Path to protein fasta file
--searchTaxa SEARCHTAXA
File containing search species line by line
--out OUT Output folder
--searchpath SEARCHPATH
Path for the search taxa directory
--corepath COREPATH Path for the core taxa directory
--annopath ANNOPATH Path for the pre-calculated feature annotion directory