hmm

integron_finder.hmm.read_hmm(replicon_id, prot_db, infile, cfg, evalue=1.0, coverage=0.5)

Function that parse hmmer –out output and returns a pandas DataFrame filter output by evalue and coverage. (Being % of the profile aligned)

Parameters:

• replicon_id (str) – the id of the replicon
• prot_db (integron_finder.prot_db.ProteinDB object.) – The protein database corresponding to the replicon translation
• infile (str) – the hmm output (in tabulated format) to parse
• cfg (integron_finder.config.Config object.) – the config
• evalue (float) – filter out hits with evalue greater tha evalue.
• coverage (float) – filter out hits with coverage under coverage (% of the profile aligned)

Returns:

data Frame with columns:

”Accession_number”, “query_name”, “ID_query”, “ID_prot”, “strand”, “pos_beg”, “pos_end”, “evalue”

each row correspond to a hit.

Return type:

a pandas.DataFrame

integron_finder.hmm.scan_hmm_bank(path)

Parameters:path (str) –

• if the path is a dir: return all files ending with .hmm in the dir
• if the path is a file: parse the file, each line must be an expression (glob) pointing to hmm files

Returns:lists of hmm files to consider for annotation Return type:list of str Raises:IOError – if the path does not exists