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

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

  • 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)

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

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