integrase

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.

Parameters
  • 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

Returns

None, the results are written on the disk