integron_finder.integrase.find_integrase(replicon_id, prot_file, out_dir, cfg)[source]

Call Prodigal for Gene annotation and hmmer to find integrase, either with phage_int HMM profile or with intI profile.

  • replicon_id (str) – The Replicon identifier to search integrase into
  • prot_file (str) – the path to the fasta file containing the translation of the replicon.
  • out_dir (str) – the relative path to the directory where prodigal outputs will be stored
  • cfg (a integron_finder.config.Config object) – the configuration

None, the results are written on the disk