annotation

integron_finder.annotation.add_feature(replicon, integron_desc, prot_db, dist_threshold)

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)

Call hmmmer to annotate CDS associated with the integron.

Use Resfams per default (Gibson et al, ISME J., 2014)

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.