utils¶
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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.
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__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.
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__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.
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__weakref__
¶ list of weak references to the object (if defined)
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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
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integron_finder.utils.
log_level
(verbose, quiet)[source]¶ - Returns
the level to apply to loggers. 0 <= level <=50
- Return type
int
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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
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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
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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.