utils¶
-
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
Warning
The sequences order is not guarantee.
-
__init__
(path, alphabet=IUPACAmbiguousDNA(), replicon_name=None, dist_threshold=4000)[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.