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.
- replicon (a
-
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)
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.
- integrons (list of