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.
- __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)
- 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_prot_fasta(path)
- Parameters
path – The path to the fasta file.
- Returns
The sequence parsed.
- Return type
Bio.SeqRecord.SeqRecord
object.