Package Bio :: Package Blast :: Module Record :: Class HSP
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Class HSP

source code

object --+
         |
        HSP

Stores information about one hsp in an alignment hit.

Members:

Not all flavors of BLAST return values for every attribute:

          score     expect     identities   positives    strand  frame
BLASTP     X          X            X            X
BLASTN     X          X            X            X          X
BLASTX     X          X            X            X                  X
TBLASTN    X          X            X            X                  X
TBLASTX    X          X            X            X                 X/X

Note: for BLASTX, the query sequence is shown as a protein sequence, but the numbering is based on the nucleotides. Thus, the numbering is 3x larger than the number of amino acid residues. A similar effect can be seen for the sbjct sequence in TBLASTN, and for both sequences in TBLASTX.

Also, for negative frames, the sequence numbering starts from query_start and counts down.

Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
source code
 
__str__(self)
str(x)
source code

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

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

source code 
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

__str__(self)
(Informal representation operator)

source code 
str(x)

Overrides: object.__str__
(inherited documentation)