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python-biopython  1.60
Public Member Functions | Public Attributes
Bio.Blast.Record.Parameters Class Reference
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Public Member Functions

def __init__

Public Attributes

 matrix
 gap_penalties
 sc_match
 sc_mismatch
 num_hits
 num_sequences
 num_good_extends
 num_seqs_better_e
 hsps_no_gap
 hsps_prelim_gapped
 hsps_prelim_gapped_attemped
 hsps_gapped
 query_id
 query_length
 database_length
 effective_hsp_length
 effective_query_length
 effective_database_length
 effective_search_space
 effective_search_space_used
 frameshift
 threshold
 window_size
 dropoff_1st_pass
 gap_x_dropoff
 gap_x_dropoff_final
 gap_trigger
 blast_cutoff

Detailed Description

Holds information about the parameters.

Members:
matrix              Name of the matrix.
gap_penalties       Tuple of (open, extend) penalties.  (floats)
sc_match            Match score for nucleotide-nucleotide comparison
sc_mismatch         Mismatch penalty for nucleotide-nucleotide comparison
num_hits            Number of hits to the database.  (int)
num_sequences       Number of sequences.  (int)
num_good_extends    Number of extensions.  (int)
num_seqs_better_e   Number of sequences better than e-value.  (int)
hsps_no_gap         Number of HSP's better, without gapping.  (int)
hsps_prelim_gapped  Number of HSP's gapped in prelim test.  (int)
hsps_prelim_gapped_attemped  Number of HSP's attempted in prelim.  (int)
hsps_gapped         Total number of HSP's gapped.  (int)
query_length        Length of the query.  (int)
query_id            Identifier of the query sequence. (str)
database_length     Number of letters in the database.  (int)
effective_hsp_length         Effective HSP length.  (int)
effective_query_length       Effective length of query.  (int)
effective_database_length    Effective length of database.  (int)
effective_search_space       Effective search space.  (int)
effective_search_space_used  Effective search space used.  (int)
frameshift          Frameshift window.  Tuple of (int, float)
threshold           Threshold.  (int)
window_size         Window size.  (int)
dropoff_1st_pass    Tuple of (score, bits).  (int, float)
gap_x_dropoff       Tuple of (score, bits).  (int, float)
gap_x_dropoff_final Tuple of (score, bits).  (int, float)
gap_trigger         Tuple of (score, bits).  (int, float)
blast_cutoff        Tuple of (score, bits).  (int, float)

Definition at line 280 of file Record.py.


Constructor & Destructor Documentation

Reimplemented in Bio.Blast.Record.PSIBlast, and Bio.Blast.Record.Blast.

Definition at line 313 of file Record.py.

00313 
00314     def __init__(self):
00315         self.matrix = ''
00316         self.gap_penalties = (None, None)
00317         self.sc_match = None
00318         self.sc_mismatch = None
00319         self.num_hits = None
00320         self.num_sequences = None
00321         self.num_good_extends = None
00322         self.num_seqs_better_e = None
00323         self.hsps_no_gap = None
00324         self.hsps_prelim_gapped = None
00325         self.hsps_prelim_gapped_attemped = None
00326         self.hsps_gapped = None
00327         self.query_id = None
00328         self.query_length = None
00329         self.database_length = None
00330         self.effective_hsp_length = None
00331         self.effective_query_length = None
00332         self.effective_database_length = None
00333         self.effective_search_space = None
00334         self.effective_search_space_used = None
00335         self.frameshift = (None, None)
00336         self.threshold = None
00337         self.window_size = None
00338         self.dropoff_1st_pass = (None, None)
00339         self.gap_x_dropoff = (None, None)
00340         self.gap_x_dropoff_final = (None, None)
00341         self.gap_trigger = (None, None)
00342         self.blast_cutoff = (None, None)
00343 
#TODO - Add a friendly __str__ method to BLAST results    

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Member Data Documentation

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The documentation for this class was generated from the following file: