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CoreBio

Package corebio :: Package ssearch_io :: Class Alignment
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Type Alignment

object --+
         |
        Alignment


An alignment between query and subject sequences. 
For BLAST, these are High scoring Segment pairs (HSPs)

raw_score        -- Typically signficance of the hit in bits, e.g. 92.0
significance     -- Typically evalue. e.g '2e-022' 

similar               -- number of conserved residues #FIXME eiter frac or num
identical         -- number of identical residues
gaps              -- number of gaps    
length            -- length of the alignment

query_seq         -- query string from alignment
target_seq        -- hit string from alignment
mid_seq               --

query_start       --
query_frame       --

target_start      --
target_frame      --
Method Summary
  __init__(self)
  __repr__(self)
    Inherited from object
  __delattr__(...)
x.__delattr__('name') <==> del x.name...
  __getattribute__(...)
x.__getattribute__('name') <==> x.name...
  __hash__(x)
x.__hash__() <==> hash(x)...
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T...
  __reduce__(...)
helper for pickle...
  __reduce_ex__(...)
helper for pickle...
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value...
  __str__(x)
x.__str__() <==> str(x)...

Class Variable Summary
list __slots__ = ['raw_score', 'bit_score', 'significance', '...
member_descriptor bit_score = <member 'bit_score' of 'Alignment' objects>
member_descriptor gaps = <member 'gaps' of 'Alignment' objects>
member_descriptor identical = <member 'identical' of 'Alignment' objects>
member_descriptor length = <member 'length' of 'Alignment' objects>
member_descriptor mid_seq = <member 'mid_seq' of 'Alignment' objects>
member_descriptor query_frame = <member 'query_frame' of 'Alignment' objec...
member_descriptor query_seq = <member 'query_seq' of 'Alignment' objects>
member_descriptor query_start = <member 'query_start' of 'Alignment' objec...
member_descriptor raw_score = <member 'raw_score' of 'Alignment' objects>
member_descriptor significance = <member 'significance' of 'Alignment' obj...
member_descriptor similar = <member 'similar' of 'Alignment' objects>
member_descriptor target_frame = <member 'target_frame' of 'Alignment' obj...
member_descriptor target_seq = <member 'target_seq' of 'Alignment' objects...
member_descriptor target_start = <member 'target_start' of 'Alignment' obj...

Class Variable Details

__slots__

Type:
list
Value:
['raw_score',
 'bit_score',
 'significance',
 'similar',
 'identical',
 'gaps',
 'length',
 'query_seq',
...

bit_score

Type:
member_descriptor
Value:
<member 'bit_score' of 'Alignment' objects>

gaps

Type:
member_descriptor
Value:
<member 'gaps' of 'Alignment' objects>

identical

Type:
member_descriptor
Value:
<member 'identical' of 'Alignment' objects>

length

Type:
member_descriptor
Value:
<member 'length' of 'Alignment' objects>

mid_seq

Type:
member_descriptor
Value:
<member 'mid_seq' of 'Alignment' objects>

query_frame

Type:
member_descriptor
Value:
<member 'query_frame' of 'Alignment' objects>

query_seq

Type:
member_descriptor
Value:
<member 'query_seq' of 'Alignment' objects>

query_start

Type:
member_descriptor
Value:
<member 'query_start' of 'Alignment' objects>

raw_score

Type:
member_descriptor
Value:
<member 'raw_score' of 'Alignment' objects>

significance

Type:
member_descriptor
Value:
<member 'significance' of 'Alignment' objects>

similar

Type:
member_descriptor
Value:
<member 'similar' of 'Alignment' objects>

target_frame

Type:
member_descriptor
Value:
<member 'target_frame' of 'Alignment' objects>

target_seq

Type:
member_descriptor
Value:
<member 'target_seq' of 'Alignment' objects>

target_start

Type:
member_descriptor
Value:
<member 'target_start' of 'Alignment' objects>

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