pip install integron_finder

usage: integron_finder [-h] [--local_max] [--func_annot] [--cpu CPU]
                       [-dt DISTANCE_THRESH] [--outdir .] [--linear]
                       [--union_integrases] [--cmsearch CMSEARCH]
                       [--hmmsearch HMMSEARCH] [--prodigal PRODIGAL]
                       [--path_func_annot bank_hmm] [--gembase]
                       [--attc_model file.cm] [--evalue_attc 1]
                       [--keep_palindromes] [--no_proteins]
                       [--max_attc_size 200] [--min_attc_size 40]
                       [--eagle_eyes] [-V]
                       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 Func_annot folder.
  --cpu CPU             Number of CPUs used by INFERNAL and HMMER
  -dt DISTANCE_THRESH, --distance_thresh DISTANCE_THRESH
                        Two elements are aggregated if they are distant of
                        DISTANCE_THRESH [4kb] or less
  --outdir .            Set the output directory (default: current)
  --linear              Consider replicon as linear. If replicon smaller than
                        20kb, it will be considered as linear
  --union_integrases    Instead of taking intersection of hits from Phage_int
                        profile (Tyr recombinases) and integron_integrase
                        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 bank_hmm
                        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
  --attc_model file.cm  path or file to the attc model (Covariance Matrix)
  --evalue_attc 1       set evalue threshold to filter out hits above it
                        (default: 1)
  --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.
  --max_attc_size 200   set maximum value fot the attC size (default: 200bp)
  --min_attc_size 40    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.
  -V, --version         show program's version number and exit

integron_finder myfastafile.fst --local_max --func_annot