Package csb :: Package bio :: Package sequence :: Module alignment :: Class AlignmentResult

Class AlignmentResult

object --+
         |
        AlignmentResult

Represents a pairwise sequence alignment result.

Instance Methods

__init__(self, score, query, subject, qstart, qend, start, end)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

__str__(self)
str(x)

source code

SequenceAlignment

alignment(self)
Returns: as a sequence alignment object

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties
int	end Subject end position
int	gaps Total number of gaps (query + subject)
int	identicals Number of identical residues
int	identity Percentage of identical residues
bool	is_empty Return True if this is an empty alignment (i.e.
int	length Alignment length (query + subject + gaps / 2)
int	qend Query end position
int	qstart Query start position
AbstractSequence	query Aligned query sequence (with gaps)
float	score Raw alignment score
int	start Subject start position
AbstractSequence	subject Aligned subject sequence (with gaps)
Inherited from `object`: `__class__`

Method Details

init(self, score, query, subject, qstart, qend, start, end)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

score (float) - raw alignment score
query (AbstractSequence) - aligned query sequence (with gaps)
subject (AbstractSequence) - aligned subject sequence (with gaps)
qstart (int) - query start position
qend (int) - query end position
start (int) - subject start position
end (int) - subject end position

Overrides: object.__init__

(inherited documentation)

str(self)
(Informal representation operator)

source code

str(x)

Overrides: object.__str__: (inherited documentation)

alignment(self)

source code

Returns: SequenceAlignment: as a sequence alignment object

Property Details

end

Subject end position

Get Method:: unreachable.end(self) - Subject end position
Type:: int

gaps

Total number of gaps (query + subject)

Get Method:: unreachable.gaps(self) - Total number of gaps (query + subject)
Type:: int

identicals

Number of identical residues

Get Method:: unreachable.identicals(self) - Number of identical residues
Type:: int

identity

Percentage of identical residues

Get Method:: unreachable.identity(self) - Percentage of identical residues
Type:: int

is_empty

Return True if this is an empty alignment (i.e. no matches)

Get Method:: unreachable.is_empty(self) - Return True if this is an empty alignment (i.e.
Type:: bool

length

Alignment length (query + subject + gaps / 2)

Get Method:: unreachable.length(self) - Alignment length (query + subject + gaps / 2)
Type:: int

qend

Query end position

Get Method:: unreachable.qend(self) - Query end position
Type:: int

qstart

Query start position

Get Method:: unreachable.qstart(self) - Query start position
Type:: int

query

Aligned query sequence (with gaps)

Get Method:: unreachable.query(self) - Aligned query sequence (with gaps)
Type:: AbstractSequence

score

Raw alignment score

Get Method:: unreachable.score(self) - Raw alignment score
Type:: float

start

Subject start position

Get Method:: unreachable.start(self) - Subject start position
Type:: int

subject

Aligned subject sequence (with gaps)

Get Method:: unreachable.subject(self) - Aligned subject sequence (with gaps)
Type:: AbstractSequence

Class AlignmentResult

__init__(self, score, query, subject, qstart, qend, start, end) (Constructor)

__str__(self) (Informal representation operator)

alignment(self)

end

gaps

identicals

identity

is_empty

length

qend

qstart

query

score

start

subject

init(self, score, query, subject, qstart, qend, start, end)
(Constructor)

str(self)
(Informal representation operator)