integron_finder.annotation.add_feature(replicon, integron_desc, prot_db, dist_threshold)[source]

Add integron annotation to the replicon.

  • replicon (a Bio.Seq.SeqRecord object.) – The Replicon to annotate
  • integron_desc (a pandas.DataFrame) – integron description
  • prot_db (a integron_finder.prot_db.ProteinDB object.) – the path to the fasta file containing the translation of the replicon.
  • dist_threshold (int) – Two elements are aggregated if they are distant of dist_threshold or less.
integron_finder.annotation.func_annot(integrons, replicon, prot_db, hmm_files, cfg, out_dir='.', evalue=10, coverage=0.5)[source]
Call hmmmer to annotate CDS associated with the integron.
Use Resfams per default (Gibson et al, ISME J., 2014)
  • integrons (list of integron_finder.integron.Integron objects.) – integrons list to annotate
  • replicon (Bio.Seq.SeqRecord object) – replicon where the integrons were found (genomic fasta file)
  • prot_db (integron.prot_db.ProteinDB object.) – the protein database corresponding to the replicon translation
  • hmm_files (List[str]) – List of path of hmm profiles to use to scan the prot_file
  • cfg (integron_finder.config.Config) – the configuration for this analyse
  • out_dir (str) – the path of the directory where to store the results
  • evalue (float) –
  • coverage (float) –


But several files per hmm file are produced.

  • subseqprot.tmp: fasta file containing a subset of protfile (the proteins belonging to the integron)
  • <hmm>_fa.res: an output of the hmm search.
  • <hmm>_fa_table.res: an output of the hmm search in tabulated format.