README.md

Installation instructions

conda install

Make idops conda environment with local package:

conda create -n idops -c gamb-go -c bioconda idops

Test installation with:

conda activate idops

idops --help

Other dependencies

Not included in the conda requirements is prokka. Please make sure to have a version of prokka installed with databases configured. Please find idops arguments with idops --help

Run IDOPS

Recommended options:

idops -o idops_out -i -t   *.gbk 

-o: output folder -i: analyse and plot genomic environment -t: add NearestNeighbor to output table and save trees of closest sequences from the official database

General Usage:

usage: idops [-h] [-v] [-o OUTPUT] [-d] [-i] [-c value] [-k] [-t] sequence_file [sequence_file ...]

IDentification Of Pesticidal Sequences

positional arguments:
  sequence_file         File(s) containing input sequences. Supported formats: *.faa [Protein], *.fasta [Protein], *.gbk [DNA with CDS Features]

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbosity       increase output verbosity
  -o OUTPUT, --output OUTPUT
                        Output directory, default 'IDOPS_{DATE_TIME}'
  -d, --disable_tc      No cutoff for hmmscan
  -i, --identify-conserved-env
                        Analyze genomic environment of hits (requires properly configured prokka) and plot Easyfig
  -c value, --cluster-cutoff value
                        Uses the value as distance cutoff for annotation distance single linkage clustering:1 (one cluster) >= value >= 0 (no clusters) , default 0.6
  -k, --keep-annotations
                        switches off the reannotation with Prokka. BEWARE: for proper genomic analysis it is crucial that the annotations are done by the same tool!
  -t, --tree            Create phylogenetic tree for each hit with the 10 closest sequences of the corresponding protein group. Adds the column 'NearestNeighbor' in summary table.