class integron_finder.utils.FastaIterator(path, alphabet=IUPACAmbiguousDNA(), replicon_name=None, dist_threshold=4000)[source]

Allow to parse over a multi fasta file, and iterate over it


The sequences order is not guarantee.

__init__(path, alphabet=IUPACAmbiguousDNA(), replicon_name=None, dist_threshold=4000)[source]
  • path (str) – The path to the file containing the sequences.
  • alphabet (Bio.SeqIUPAC member) – The authorized alphabet
  • replicon_name (str) – The name of the replicon, if this specify all sequence.name will have this value
  • dist_threshold (int) – The minimum length for a replicon to be considered as circular. Under this threshold even the provided topology is ‘circular’ the computation will be done with a ‘linear’ topology.
Returns:The number of sequence in the file
Returns:The next sequence (the order of sequences is not guaranteed).
Return type:a Bio.SeqRecord object or None if the sequence is not compliant with the alphabet.

list of weak references to the object (if defined)

Parameters:seq (Bio.Seq.Seq instance) – the sequence to check
Returns:True if sequence letters are a subset of the alphabet, False otherwise.
Parameters:topologies (integron_finder.Topology onject) –
Parameters:path – The path to extract name for instance the fasta file to the replicon
Returns:the name of replicon for instance if path = /path/to/replicon.fasta name = replicon
integron_finder.utils.log_level(verbose, quiet)[source]
Returns:the level to apply to loggers. 0 <= level <=50
Return type:int

fasta generator maker

Parameters:alphabet – the alphabet store in the fasta generator closure
Returns:generator to iterate on the fasta file in the same order as in fasta file
Parameters:path (str) – the path to the covariance model file
Returns:the length of the model
Return type:int
Parameters:path – The path to the fasta file.
Returns:The sequence parsed.
Return type:Bio.SeqRecord.SeqRecord object.