Integron Finder

Finds integrons in DNA sequences

You can use it in command line, see installation below, or you can use it online on the Galaxy Pasteur.

See Documentation for how to use it:

Installation

Although a system wide installation is possible and supported, many distribution do not allow it. So we describe bellow some user wide installation procedures.

For user

pip install --user integron_finder==2.xx

for more installation options, or for developer installation see documentation

In a virtualenv

To avoid interaction with the system libraries you can install integron_finder in a virtualenv.

1. create and activate the virtualenv bash python -m venv Integron_Finder ./Integron_Finder/bin/activate
2. install integronfinder ```bash (IntegronFinder) python -m pip install integronfinder `` all libraries will be located inIntegronFinder` directory
3. when you want to quit the virtualenv bash (Integron_Finder) deactivate

Container

For reproducibility and easy way to use integron_finder without installing third party software (hmmsearch, prodigal, ...) or libraries, we provide containers based on docker.

https://hub.docker.com/r/gempasteur/integron_finder

Docker

The computation are perform under IF user in /home/IF inside the container. So You have to mount a directory from the host in the container to exchange data (inputs data, and results) from the host and the container.

The shared directory must be writable by the IF user or overwrite the user in the container by your id (see example below)

mkdir shared_dir cd shared_dir docker run -v $PWD:/home/IF -u $(id -u ${USER}):$(id -g ${USER}) integron_finder:2.0rc9 --local-max --circ --keep-tmp NZ_CP016323.fna

Singularity

As the docker image is registered in docker hub you can also use it directly with Singularity. Unlike docker, you have not to worry about shared directory, your home and /tmp are automatically shared.

singularity run -H ${HOME} docker://gempasteur/integron_finder:2.0rc9 --local-max --circ --keep-tmp NZ_CP016323.fna

or use -b option if the data is not in your home.

singularity run -H ${HOME} -b <the directory containing data> docker://gempasteur/integron_finder:2.0rc9 --local-max --circ --keep-tmp NZ_CP016323.fna

Conda installation

From 2.0 version, IntegronFinder is available as conda package. Integronfinder is in bioconda channel. (The advantage with this solution is that it will install prodigal, hmmer, and infernal too.)

1. install conda

2. Set up channels:

   conda config --add channels defaults
   conda config --add channels conda-forge
   conda config --add channels bioconda
   

3. install integron_finder:

   conda install integron_finder
   

For developer

If you want to develop or submit a patch on this software you are welcome. See Developer installation in documentation.

Licence:

• Integron Finder is developed and released under open source licence GPLv3 (see COPYING file)
• NCBIfam-AMRFinder is provided by NCBI and accessible here: https://ftp.ncbi.nlm.nih.gov/hmm/NCBIfam-AMRFinder/2021-06-01.1/NCBIfam-AMRFinder.LIB
• The other data files:
  • attc_4.cm
  • integron_integrase.hmm
  • phage-int.hmm
    are licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

Contributing

We encourage contributions, bug report, enhancement ...

But before to do that we encourage to read the contributing guide.

Dependencies

• Python >=3.10
• Pandas >=2
• Numpy >=1.26
• Biopython >=1.82
• Matplotlib >=3.8
• colorlog
• HMMER >=3.1b2,<=3.3.2
• INFERNAL >=1.1.2,<=1.1.4
• Prodigal >=2.6.2,<=V2.6.3

Usage

``` usage: integron_finder [-h] [--local-max] [--func-annot] [--cpu CPU] [-dt DISTANCE_THRESHOLD] [--outdir OUTDIR] [--union-integrases] [--cmsearch CMSEARCH] [--hmmsearch HMMSEARCH] [--prodigal PRODIGAL] [--path-func-annot PATHFUNCANNOT] [--gembase] [--gembase-path GEMBASE_PATH] [--annot-parser ANNOT_PARSER] [--prot-file PROT_FILE] [--attc-model ATTC_MODEL] [--evalue-attc EVALUE_ATTC] [--calin-threshold CALIN_THRESHOLD] [--keep-palindromes] [--no-proteins] [--promoter-attI] [--max-attc-size MAXATTCSIZE] [--min-attc-size MINATTCSIZE] [--eagle-eyes] [--pdf] [--gbk] [--keep-tmp] [--split-results] [--circ | --linear] [--topology-file TOPOLOGY_FILE] [--version] [--mute] [-v] [-q] replicon

positional arguments: replicon Path to the replicon file (in fasta format), eg : path/to/file.fst or file.fst

optional arguments: -h, --help show this help message and exit --local-max Allows thorough local detection (slower but more sensitive and do not increase false positive rate). --func-annot Functional annotation of CDS associated with integrons HMM files are needed in Funcannot folder. --cpu CPU Number of CPUs used by INFERNAL and HMMER. Increasing too much (usually above 4) may decrease performance. -dt DISTANCETHRESHOLD, --distance-thresh DISTANCETHRESHOLD Two elements are aggregated if they are distant of DISTANCETHRESH [4000]bp or less --outdir OUTDIR Set the output directory (default: current) --union-integrases Instead of taking intersection of hits from Phageint profile (Tyr recombinases) and integronintegrase profile, use the union of the hits --cmsearch CMSEARCH Complete path to cmsearch if not in PATH. eg: /usr/local/bin/cmsearch --hmmsearch HMMSEARCH Complete path to hmmsearch if not in PATH. eg: /usr/local/bin/hmmsearch --prodigal PRODIGAL Complete path to prodigal if not in PATH. eg: /usr/local/bin/prodigal --path-func-annot PATHFUNCANNOT Path to file containing all hmm bank paths (one per line) --gembase Use gembase formatted protein file instead of Prodigal. Folder structure must be preserved --gembase-path GEMBASEPATH path to the gembase root directory (needed only if the replicon file is not locatedin gembase-path) --annot-parser ANNOTPARSER the path to the parser to use to get information from protein file. --prot-file PROTFILE The path to the proteins file used for annotations --attc-model ATTCMODEL Path or file to the attc model (Covariance Matrix). --evalue-attc EVALUEATTC Set evalue threshold to filter out hits above it (default: 1) --calin-threshold CALINTHRESHOLD keep 'CALIN' only if attC sites number >= calin-threshold (default: 2) --keep-palindromes For a given hit, if the palindromic version is found, don't remove the one with highest evalue. --no-proteins Don't annotate CDS and don't find integrase, just look for attC sites. --promoter-attI Search also for promoter and attI sites. (default False) --max-attc-size MAXATTCSIZE Set maximum value fot the attC size (default: 200bp) --min-attc-size MINATTCSIZE set minimum value fot the attC size (default: 40bp) --eagle-eyes Synonym of --local-max. Like a soaring eagle in the sky, catching rabbits (or attC sites) by surprise. --circ Set the default topology for replicons to 'circular' --linear Set the default topology for replicons to 'linear' --topology-file TOPOLOGYFILE The path to a file where the topology for each replicon is specified. --version show program's version number and exit --mute mute the log on stdout.(continue to log on integronfinder.out)

Output options: --pdf For each complete integron, a simple graphic of the region is depicted (in pdf format) --gbk generate a GenBank file with the sequence annotated with the same annotations than .integrons file. --keep-tmp keep intermediate results. This results are stored in directory named tmp_ --split-results Instead of merging integron results from all replicon in one file, keep them in separated files.

-v, --verbose Increase verbosity of output (can be cumulative : -vv) -q, --quiet Decrease verbosity of output (can be cumulative : -qq)

```

Example

integron_finder --local-max --func-annot mysequences.fst

Output :

By default, integronfinder will output 3 files under ResultsIntegronFindermysequences:

• mysequences.integrons : A file with all integrons and their elements detected in all sequences in the input file.
• mysequences.summary : A summary file with the number and type of integrons per sequence.
• integron_finder.out : A copy standard output. The stdout can be silenced with the argument --mute

The amount of log in the standard output can be controlled with --verbose for more or --quiet for less, and both are cumulative arguments, eg. -vv or -qq.

Other files can be created on demand:

• --gbk: Creates a Genbank files with all the annotations found (present in the .integrons file)
• --pdf: Creates a simple pdf graphic with complete integrons
• --keep-tmp: Keep temporary files. See Keep intermediate files for more.

Galaxy

You can use this program without installing it, through the pasteur galaxy webserver instance:

• Galaxy Pasteur

Citation

The paper is published in Microorganism.

Néron, Bertrand, Eloi Littner, Matthieu Haudiquet, Amandine Perrin, Jean Cury, and Eduardo P.C. Rocha. 2022. IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella Microorganisms 10, no. 4: 700. https://doi.org/10.3390/microorganisms10040700

Please cite also the following articles:

• Nawrocki, E.P. and Eddy, S.R. (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29, 2933-2935.
• Eddy, S.R. (2011) Accelerated Profile HMM Searches. PLoS Comput Biol, 7, e1002195.
• Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W. and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.

and if you use the function --func_annot which uses NCBIfam-AMRFinder hmm profiles:

• Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860 PMID: 29112715