annotation

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

Add integron annotation to the replicon.

Parameters
  • 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 NCBIfam-AMRFinder.LIB available here https://ftp.ncbi.nlm.nih.gov/hmm/NCBIfam-AMRFinder/
check for the appropriate version
Parameters
  • 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) –

Returns

None.

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.