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 annotateintegron_desc (a
pandas.DataFrame
) – integron descriptionprot_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 annotatereplicon (
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 translationhmm_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 analyseout_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.