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

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object --+
         |
        HSP

Stores information about one hsp in an alignment hit.

Members:
score           BLAST score of hit.  (float)
bits            Number of bits for that score.  (float)
expect          Expect value.  (float)
num_alignments  Number of alignments for same subject.  (int)
identities      Number of identities (int) if using the XML parser.
                Tuple of numer of identities/total aligned (int, int)
                if using the (obsolete) plain text parser.
positives       Number of positives (int) if using the XML parser.
                Tuple of numer of positives/total aligned (int, int)
                if using the (obsolete) plain text parser.
gaps            Number of gaps (int) if using the XML parser.
                Tuple of numer of gaps/total aligned (int, int) if
                using the (obsolete) plain text parser.
align_length    Length of the alignment. (int)
strand          Tuple of (query, target) strand.
frame           Tuple of 1 or 2 frame shifts, depending on the flavor.

query           The query sequence.
query_start     The start residue for the query sequence.  (1-based)
query_end       The end residue for the query sequence.  (1-based)
match           The match sequence.
sbjct           The sbjct sequence.
sbjct_start     The start residue for the sbjct sequence.  (1-based)
sbjct_end       The end residue for the sbjct sequence.  (1-based)

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 help(type(x)) 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 help(type(x)) for signature

Overrides: object.__init__
(inherited documentation)

__str__(self)
(Informal representation operator)

source code 
str(x)

Overrides: object.__str__
(inherited documentation)