utils

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

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

Warning

The sequences order is not guarantee.

__init__(path, replicon_name=None, dist_threshold=4000, alphabet=None)[source]
Parameters
  • 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.

__len__()[source]
Returns

The number of sequence in the file

__next__()[source]
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.

__weakref__

list of weak references to the object (if defined)

_check_seq_alphabet_compliance(seq)[source]
Parameters

seq (Bio.Seq.Seq instance) – the sequence to check

Returns

True if sequence letters are a subset of the alphabet, False otherwise.

_set_topologies(topologies)[source]
Parameters

topologies (integron_finder.Topology onject) –

Returns

integron_finder.utils.get_name_from_path(path)[source]
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

integron_finder.utils.make_multi_fasta_reader(alphabet)[source]

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

integron_finder.utils.model_len(path)[source]
Parameters

path (str) – the path to the covariance model file

Returns

the length of the model

Return type

int

integron_finder.utils.read_multi_fasta(path)
Parameters

path – The path to the fasta file.

Returns

The sequence parsed.

Return type

Bio.SeqRecord.SeqRecord object.