[BioRuby-cvs] bioruby/lib/bio/appl/blast wublast.rb,1.2,1.3
Naohisa Goto
ngoto at pub.open-bio.org
Mon Oct 31 14:24:16 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory pub.open-bio.org:/tmp/cvs-serv4472
Modified Files:
wublast.rb
Log Message:
Added Rdoc documentation.
Fixed bug in F0dbstat#parse_dbstat.
Catch up changes in format0.rb.
Index: wublast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** wublast.rb 8 Sep 2005 01:22:08 -0000 1.2
--- wublast.rb 31 Oct 2005 19:24:14 -0000 1.3
***************
*** 1,7 ****
#
! # bio/appl/blast/wublast.rb - WU-BLAST default output parser
#
! # Copyright (C) 2003 GOTO Naohisa <ng at bioruby.org>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
--- 1,9 ----
#
! # = bio/appl/blast/wublast.rb - WU-BLAST default output parser
#
! # Copyright:: Copyright (C) 2003 GOTO Naohisa <ng at bioruby.org>
! # Licence:: LGPL
#
+ #--
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
***************
*** 17,32 ****
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id$
#
require 'bio/appl/blast/format0'
! module Bio
! class Blast
! module WU
class Report < Default::Report
def parameters
parse_parameters
--- 19,52 ----
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ #++
#
# $Id$
#
+ # WU-BLAST default output parser.
+ #
+ # The parser is still incomplete and may contain many bugs,
+ # because I didn't have WU-BLAST license.
+ # It was tested under web-based WU-BLAST results and
+ # obsolete version downloaded from http://blast.wustl.edu/ .
+ #
+ # = References
+ # * http://blast.wustl.edu/
+ # * http://www.ebi.ac.uk/blast2/
+ #
require 'bio/appl/blast/format0'
! module Bio #:nodoc:
! class Blast #:nodoc:
! module WU #:nodoc:
+ # Bio::Blast::WU::Report parses WU-BLAST default output
+ # and stores information in the data.
+ # It may contain a Bio::Blast::WU::Report::Iteration object.
+ # Because it inherits Bio::Blast::Default::Report,
+ # please also refer Bio::Blast::Default::Report.
class Report < Default::Report
+ # Returns parameters (???)
def parameters
parse_parameters
***************
*** 34,37 ****
--- 54,58 ----
end
+ # Returns parameter matrix (???)
def parameter_matrix
parse_parameters
***************
*** 39,44 ****
--- 60,67 ----
end
+ # Returns e-value threshold specified when BLAST was executed.
def expect; parse_parameters; @parameters['E']; end
+ # Returns warning messages.
def warnings
unless defined?(@warnings)
***************
*** 49,52 ****
--- 72,76 ----
end
+ # Returns notice messages.
def notice
unless defined?(@notice)
***************
*** 57,60 ****
--- 81,85 ----
private
+ # Splits headers.
def format0_split_headers(data)
@f0header = data.shift
***************
*** 80,87 ****
--- 105,114 ----
end
+ # Splits search data.
def format0_split_search(data)
[ Iteration.new(data) ]
end
+ # Splits statistics parameters.
def format0_split_stat_params(data)
@f0warnings = []
***************
*** 100,106 ****
@f0dbstat = F0dbstat.new(@f0wu_stats)
itr = @iterations[0]
! itr.f0dbstat = @f0dbstat if itr
end
def parse_parameters
unless defined?(@parse_parameters)
--- 127,135 ----
@f0dbstat = F0dbstat.new(@f0wu_stats)
itr = @iterations[0]
! x = @f0dbstat
! itr.instance_eval { @f0dbstat = x } if itr
end
+ # Splits parameters.
def parse_parameters
unless defined?(@parse_parameters)
***************
*** 126,130 ****
end
! class F0dbstat < Default::Report::F0dbstat
def initialize(ary)
@f0stat = ary
--- 155,161 ----
end
! # Stores database statistics.
! # Internal use only. Users must not use the class.
! class F0dbstat < Default::Report::F0dbstat #:nodoc:
def initialize(ary)
@f0stat = ary
***************
*** 132,145 ****
end
#undef :f0params
#undef :matrix, :gap_open, :gap_extend,
# :eff_space, :expect, :sc_match, :sc_mismatch,
# :num_hits
def parse_dbstat
unless defined?(@parse_dbstat)
! @f0stat.each do |x|
! parse_colon_separated(@hash, x)
! end
@database = @hash['Database']
@posted_date = @hash['Posted']
--- 163,177 ----
end
+ #--
#undef :f0params
#undef :matrix, :gap_open, :gap_extend,
# :eff_space, :expect, :sc_match, :sc_mismatch,
# :num_hits
+ #++
+ # Parses database statistics.
def parse_dbstat
unless defined?(@parse_dbstat)
! parse_colon_separated_params(@hash, @f0stat)
@database = @hash['Database']
@posted_date = @hash['Posted']
***************
*** 157,167 ****
end #class F0dbstat
! class Frame
! end #class FrameParams
class Iteration < Default::Report::Iteration
def initialize(data)
@f0stat = []
! @f0dbstat = nil
@f0hitlist = []
@hits = []
--- 189,212 ----
end #class F0dbstat
! #--
! #class Frame
! #end #class FrameParams
! #++
+ # Iteration class for WU-BLAST report.
+ # Though WU-BLAST does not iterate like PSI-BLAST,
+ # Bio::Blast::WU::Report::Iteration aims to keep compatibility
+ # with Bio::Blast::Default::Report::* classes.
+ # It may contain some Bio::Blast::WU::Report::Hit objects.
+ # Because it inherits Bio::Blast::Default::Report::Iteration,
+ # please also refer Bio::Blast::Default::Report::Iteration.
class Iteration < Default::Report::Iteration
+ # Creates a new Iteration object.
+ # It is designed to be called only internally from
+ # the Bio::Blast::WU::Report class.
+ # Users shall not use the method directly.
def initialize(data)
@f0stat = []
! @f0dbstat = Default::Report::AlwaysNil.instance
@f0hitlist = []
@hits = []
***************
*** 183,186 ****
--- 228,232 ----
end
+ # Returns warning messages.
def warnings
@f0warnings
***************
*** 188,191 ****
--- 234,238 ----
private
+ # Parses hit list.
def parse_hitlist
unless defined?(@parse_hitlist)
***************
*** 232,236 ****
--- 279,292 ----
end #class Iteration
+ # Bio::Blast::WU::Report::Hit contains information about a hit.
+ # It may contain some Bio::Blast::WU::Report::HSP objects.
+ #
+ # Because it inherits Bio::Blast::Default::Report::Hit,
+ # please also refer Bio::Blast::Default::Report::Hit.
class Hit < Default::Report::Hit
+ # Creates a new Hit object.
+ # It is designed to be called only internally from the
+ # Bio::Blast::WU::Report::Iteration class.
+ # Users should not call the method directly.
def initialize(data)
@f0hitname = data.shift
***************
*** 250,266 ****
end
def score
@score
end
! attr_reader :pvalue, :n_number
end #class Hit
class HSP < Default::Report::HSP
! method_after_parse_score :pvalue, :p_sum_n
end #class HSP
end #class Report
class Report_TBlast < Report
DELIMITER = RS = "\nTBLAST"
end #class Report_TBlast
--- 306,340 ----
end
+ # Returns score.
def score
@score
end
! # p-value
! attr_reader :pvalue
! # n-number (???)
! attr_reader :n_number
end #class Hit
+ # Bio::Blast::WU::Report::HSP holds information about the hsp
+ # (high-scoring segment pair).
+ #
+ # Because it inherits Bio::Blast::Default::Report::HSP,
+ # please also refer Bio::Blast::Default::Report::HSP.
class HSP < Default::Report::HSP
! # p-value
! attr_reader :pvalue if false #dummy
! method_after_parse_score :pvalue
! # p_sum_n (???)
! attr_reader :p_sum_n if false #dummy
! method_after_parse_score :p_sum_n
end #class HSP
end #class Report
+ # WU-BLAST default output parser for TBLAST.
+ # All methods are equal to Bio::Blast::WU::Report.
+ # Only DELIMITER (and RS) is different.
class Report_TBlast < Report
+ # Delimter of each entry for TBLAST. Bio::FlatFile uses it.
DELIMITER = RS = "\nTBLAST"
end #class Report_TBlast
***************
*** 478,501 ****
######################################################################
- =begin
-
- = Bio::Blast::WU::Report
-
- WU-BLAST default output parser.
- It is still incomplete and may contain many bugs,
- because I don't have WU-BLAST license.
- It was tested under web-based WU-BLAST results and
- obsolete version downloaded from ((<URL:http://blast.wustl.edu/>)).
-
- = Bio::Blast::WU::Report_TBlast
-
- WU-BLAST default output parser for TBLAST.
- All methods are equal to Bio::Blast::WU::Report.
- Only DELIMITER (and RS) is different.
-
- = References
-
- * ((<URL:http://blast.wustl.edu/>))
- * ((<URL:http://www.ebi.ac.uk/blast2/>))
-
- =end
--- 552,553 ----
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