Classes¶

This module stores the classes (Organism, Scaffold, Hit) used in cblaster.

class cblaster.classes.Hit(query, subject, identity, coverage, evalue, bitscore)¶

A BLAST hit identified during a cblaster search.

This class is first instantiated when parsing BLAST results, and is then updated with genomic coordinates after querying either the Identical Protein Groups (IPG) resource on NCBI, or a local JSON database.

query¶

Name of query sequence.

Type:	str

subject¶

Name of subject sequence.

Type:	str

identity¶

Percentage identity (%) of hit.

Type:	float

coverage¶

Query coverage (%) of hit.

Type:	float

evalue¶

E-value of hit.

Type:	float

bitscore¶

Bitscore of hit.

Type:	float

start¶

Start of subject sequence on corresponding scaffold.

Type:	int

end¶

End of subject sequence on corresponding scaffold

Type:	int

strand¶

Orientation of subject sequence (‘+’ or ‘-‘).

Type:	str

copy(**kwargs)¶: Creates a copy of this Hit with any additional args.

classmethod from_dict(d)¶: Loads class from dict.

to_dict()¶: Serialises class to dict.

values(decimals=4)¶

Formats hit attributes for printing.

Parameters:	decimals (int) – Total decimal places to show in score values.
Returns:	List of formatted attribute strings.

class cblaster.classes.Organism(name, strain, scaffolds=None)¶

A unique organism containing hits found in a cblaster search.

Every strain (or lack thereof) is a unique Organism, and will be reported separately in cblaster results.

name¶

Organism name, typically the genus and species epithet.

Type:	str

strain¶

Strain name of this organism, e.g. CBS 536.65.

Type:	str

scaffolds¶

Scaffold objects belonging to this organism.

Type:	dict

classmethod from_dict(d)¶: Loads class from dict.

full_name¶: The full name (including strain) of the organism. Note: if strain found in name, returns just name.

to_dict()¶: Serialises class to dict.

total_hit_clusters¶: Counts total amount of hit clusters in this Organism.

class cblaster.classes.Scaffold(accession, clusters=None, subjects=None)¶

A genomic scaffold containing hits found in a cblaster search.

accession¶

Name of this scaffold, typically NCBI accession.

Type:	str

hits¶

Hit objects located on this scaffold.

Type:	list

clusters¶

Clusters of hits identified on this scaffold.

Type:	list

classmethod from_dict(d)¶: Loads class from dict.

to_dict()¶: Serialises class to dict.

class cblaster.classes.Serializer¶

JSON serialisation mixin class.

Classes that inherit from this class should implement to_dict and from_dict methods.

classmethod from_dict(d)¶: Loads class from dict.

classmethod from_json(js)¶: Instantiates class from JSON handle.

to_dict()¶: Serialises class to dict.

to_json(fp=None, **kwargs)¶: Serialises class to JSON.

class cblaster.classes.Session(queries, params, organisms=None)¶

Stores the state of a cblaster search.

This class stores query proteins, search parameters, Organism objects created during searches, as well as methods for generating summary tables. It can also be dumped to/loaded from JSON for re-filtering, plotting, etc.

>>> s = Session()
>>> with open("session.json", "w") as fp:
...     s.to_json(fp)
>>> with open("session.json") as fp:
...     s2 = Session.from_json(fp)
>>> s == s2
True

queries¶

Names of query sequences.

Type:	list

params¶

Search parameters.

Type:	dict

organisms¶

Organism objects created in a search.

Type:	list

format(form, fp=None, **kwargs)¶

Generates a summary table.

Parameters:	form (str) – Type of table to generate (‘summary’ or ‘binary’). fp (file handle) – File handle to write to. human (bool) – Use human-readable format. headers (bool) – Show table headers.
Raises:	`ValueError` – form not ‘binary’ or ‘summary’
Returns:	Summary table.

classmethod from_dict(d)¶: Loads class from dict.

to_dict()¶: Serialises class to dict.

class cblaster.classes.Subject(hits=None, ipg=None, start=None, end=None, strand=None)¶

A sequence representing one or more BLAST hits.

This class is instantiated during the contextual lookup stage. It is important since it allows for subject sequences which hit >1 of the query sequences, while still staying non-redundant.

hits¶

Hit objects referencing this subject sequence.

Type:	list

ipg¶

NCBI Identical Protein Group (IPG) id.

Type:	int

start¶

Start of sequence on parent scaffold.

Type:	int

end¶

End of sequence on parent scaffold.

Type:	int

strand¶

Strandedness of the sequence (‘+’ or ‘-‘).

Type:	str

classmethod from_dict(d)¶: Loads class from dict.

to_dict()¶: Serialises class to dict.