Package csb :: Package bio :: Package hmm :: Class HHpredHitAlignment

Class HHpredHitAlignment

                object --+        
                         |        
sequence.AbstractAlignment --+    
                             |    
    sequence.SequenceAlignment --+
                                 |
                                HHpredHitAlignment

Represents a query-template alignment in an HHpred result.

Nested Classes
Inherited from `sequence.AbstractAlignment`: `__metaclass__`

Instance Methods

__init__(self, hit, query, subject)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

csb.bio.sequence.A3MAlignment

to_a3m(self)
Returns: a query-centric A3M alignment.

source code

Inherited from sequence.AbstractAlignment: __getitem__, __iter__, add, format, gap_at, subregion

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

Static Methods
Inherited from `sequence.SequenceAlignment`: `parse`

Class Variables
	GAP = `GAP`
Inherited from `sequence.SequenceAlignment`: `__abstractmethods__`

Properties
str	query Query sequence (with gaps)
generator	segments Find all ungapped query-subject segments in the alignment.
str	subject Subject sequence (with gaps)
Inherited from `sequence.AbstractAlignment`: `columns`, `length`, `rows`, `size` Inherited from `object`: `__class__`

Method Details

init(self, hit, query, subject)
(Constructor)

source code

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

Parameters:

hit - relevant hit object
query (str) - the query sequence in the alignment region, with gaps
subject (str) - the subject sequence in the alignment region, with gaps

Overrides: object.__init__

(inherited documentation)

to_a3m(self)

source code

Returns: csb.bio.sequence.A3MAlignment: a query-centric A3M alignment.

Property Details

query

Query sequence (with gaps)

Get Method:: unreachable.query(self) - Query sequence (with gaps)
Type:: str

segments

Find all ungapped query-subject segments in the alignment. Return a generator over all ungapped alignment segments, represented by HHpredHit objects

Get Method:: unreachable.segments(self) - Find all ungapped query-subject segments in the alignment.
Type:: generator

subject

Subject sequence (with gaps)

Get Method:: unreachable.subject(self) - Subject sequence (with gaps)
Type:: str

Class HHpredHitAlignment

__init__(self, hit, query, subject) (Constructor)

to_a3m(self)

query

segments

subject

init(self, hit, query, subject)
(Constructor)