Module Expr Str Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str ClassDef bases NameLoad body Assign NameStore Dict Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Num Num Num Num Num Str Str Str Str FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr ListLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Expr Call AttributeLoad NameLoad attr Str For NameStore Call NameLoad Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad BinOpAdd NameLoad Num Call AttributeLoad NameLoad attr NameLoad Str Call AttributeLoad NameLoad attr NameLoad Str Call AttributeLoad NameLoad attr NameLoad Str Call AttributeLoad NameLoad attr NameLoad Str Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr NameLoad Return Call AttributeLoad Str attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad For NameStore Call NameLoad Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad Call AttributeLoad NameLoad attr NameLoad Str Call AttributeLoad NameLoad attr NameLoad Str Call AttributeLoad NameLoad attr NameLoad Str Call AttributeLoad NameLoad attr NameLoad Str Return Call AttributeLoad Str attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body If CompareNotEq Call NameLoad NameLoad Num body Raise NameLoad Str Assign NameStore ListLoad Num Num Num Num For NameStore Call AttributeLoad NameLoad attr body Assign SubscriptStore NameLoad Index Call AttributeLoad NameLoad attr NameLoad SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Return SubscriptLoad AttributeLoad NameLoad attr Index NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Return SubscriptLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Index Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr ListLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Str For NameStore Call NameLoad Num body If CompareEq SubscriptLoad NameLoad Index NameLoad NameLoad body AugAssignAdd NameStore SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Return SubscriptLoad NameLoad Index NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Assign NameStore Str For NameStore Call NameLoad Num body If CompareGtE SubscriptLoad NameLoad Index NameLoad Num body AugAssignAdd NameStore SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Return SubscriptLoad NameLoad Index NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Num Assign NameStore Str For NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad If CompareNotEq NameLoad Num body AugAssignAdd NameStore BinOpMult NameLoad Call AttributeLoad NameLoad attr NameLoad Num Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num For NameStore Call NameLoad Call NameLoad NameLoad body AugAssignAdd NameStore Call AttributeLoad NameLoad attr NameLoad Return NameLoad decorator_list decorator_list
N/A N/A Module Description

Copyright (c) 2008 Zhenhua Wu <jeremywu@jimmy.harvard.edu>

This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file COPYING included with
the distribution).

@status:  experimental
@version: $Revision$
@author:  Zhenhua Wu
@contact: jeremywu@jimmy.harvard.edu
 N/A ambiguous_nucleotide_code_codec N/A A C G T M R W S Y K V H D B N AC AG AT CG CT GT ACG ACT AGT CGT ACGT A C G T AC AG AT CG CT GT ACG ACT AGT CGT ACGT M R W S Y K V H D B N pwMatrix N/A object N/A N/A nucleotide_column N/A A C G T a c g t 0 1 2 3 0 1 2 3 0 1 2 3 A C G T __init__ N/A N/A self N/A N/A N/A N/A self pwm N/A N/A __str__ N/A N/A self N/A N/A N/A lines N/A N/A N/A N/A lines append 	A	C	G	T	Con.	Deg. N/A index N/A range N/A len self N/A N/A N/A N/A lines append N/A %d	%.4f	%.4f	%.4f	%.4f	%s	%s N/A N/A index 1 N/A N/A self getProbabilityWeight index A N/A N/A self getProbabilityWeight index C N/A N/A self getProbabilityWeight index G N/A N/A self getProbabilityWeight index T N/A N/A self consensus index N/A N/A self degenerate index N/A N/A N/A join lines N/A toDBstring N/A N/A self N/A N/A N/A lines N/A N/A index N/A range N/A len self N/A N/A N/A N/A lines append N/A %.4f	%.4f	%.4f	%.4f N/A N/A N/A self getProbabilityWeight index A N/A N/A self getProbabilityWeight index C N/A N/A self getProbabilityWeight index G N/A N/A self getProbabilityWeight index T N/A N/A N/A join lines N/A append N/A N/A self nucleotide_weight_dict N/A N/A N/A N/A N/A len nucleotide_weight_dict 4 N/A N/A Exception The parameter should have length of 4! N/A row N/A 0 0 0 0 N/A nucleotide N/A N/A nucleotide_weight_dict keys N/A N/A N/A row N/A N/A N/A self __getColumn__ nucleotide N/A nucleotide_weight_dict N/A nucleotide N/A N/A N/A N/A self pwm append row N/A __getColumn__ N/A N/A self nucleotide N/A N/A N/A N/A N/A pwMatrix nucleotide_column N/A nucleotide N/A getProbabilityWeight N/A N/A self position nucleotide N/A N/A N/A N/A N/A N/A self pwm N/A position N/A N/A N/A self __getColumn__ nucleotide N/A __len__ N/A N/A self N/A N/A N/A N/A len N/A self pwm N/A clear N/A N/A self N/A N/A N/A N/A self pwm N/A N/A consensus N/A N/A self position N/A N/A N/A weightRow N/A N/A self pwm N/A position N/A maxP N/A max weightRow N/A baseWithMaxP N/A index N/A range 4 N/A N/A N/A N/A weightRow N/A index maxP N/A N/A baseWithMaxP N/A N/A pwMatrix nucleotide_column N/A index N/A N/A ambiguous_nucleotide_code_codec N/A baseWithMaxP N/A degenerate N/A N/A self position N/A N/A N/A weightRow N/A N/A self pwm N/A position N/A degenerateBases N/A index N/A range 4 N/A N/A N/A N/A weightRow N/A index 0.25 N/A N/A degenerateBases N/A N/A pwMatrix nucleotide_column N/A index N/A N/A ambiguous_nucleotide_code_codec N/A degenerateBases N/A getICat N/A N/A self position N/A N/A N/A ic 2.0 N/A letters ACGT N/A letter letters N/A N/A p N/A N/A self getProbabilityWeight position letter N/A N/A p 0 N/A N/A ic N/A p N/A N/A math log p 2 N/A ic N/A getIC N/A N/A self N/A N/A N/A total_ic 0 N/A position N/A range N/A len self N/A N/A total_ic N/A N/A self getICat position N/A total_ic N/A N/A