[BioRuby-cvs] bioruby/lib/bio/appl/psort report.rb,1.9,1.10
Mitsuteru C. Nakao
nakao at pub.open-bio.org
Mon Oct 31 08:13:37 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/appl/psort
In directory pub.open-bio.org:/tmp/cvs-serv32395/lib/bio/appl/psort
Modified Files:
report.rb
Log Message:
* Updated RDoc.
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/psort/report.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** report.rb 9 Sep 2005 15:48:17 -0000 1.9
--- report.rb 31 Oct 2005 13:13:35 -0000 1.10
***************
*** 1,6 ****
#
! # bio/appl/psort/report.rb - PSORT systems report classes
#
! # Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
#
# This library is free software; you can redistribute it and/or
--- 1,13 ----
#
! # = bio/appl/psort/report.rb - PSORT systems report classes
#
! # Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License:: LGPL
! #
! # $Id$
! #
! # == A Report classes for PSORT Systems
! #
! #--
#
# This library is free software; you can redistribute it and/or
***************
*** 18,22 ****
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! # $Id$
#
--- 25,29 ----
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! # ++
#
***************
*** 31,44 ****
class PSORT1
class Report
! def self.parser(str)
! self.default_parser(str)
end
!
! def self.default_parser(str)
rpt = self.new
! rpt.raw = str
query_info = str.scan(/^Query Information\n\n(.+?)\n\n/m)[0][0].split(/\n/)
result_info = str.scan(/^Result Information\n\n(.+?)\n\n\*/m)[0][0]
--- 38,56 ----
class PSORT1
+ # = Bio::PSORT::PSORT1::Report
+ # Parser class for PSORT1 output report.
+ #
+ # == Example
class Report
! # Returns aBio::PSORT::PSORT1::Report.
! def self.parser(output_report)
! self.default_parser(output_report)
end
! # Returns aBio::PSORT::PSORT1::Report.
! def self.default_parser(output_report)
rpt = self.new
! rpt.raw = output_report
query_info = str.scan(/^Query Information\n\n(.+?)\n\n/m)[0][0].split(/\n/)
result_info = str.scan(/^Result Information\n\n(.+?)\n\n\*/m)[0][0]
***************
*** 62,66 ****
end
! # new
def initialize(entry_id = '', origin = '', title = '', sequence = '',
result_info = '', reasoning = {}, final_result = [])
--- 74,89 ----
end
! attr_accessor :entry_id
! attr_accessor :origin
! attr_accessor :title
! attr_accessor :sequence
! attr_accessor :result_info
! attr_accessor :reasoning
! attr_accessor :final_result
! attr_accessor :raw
!
!
!
! # Constructs aBio::PSORT::PSORT1::Report object.
def initialize(entry_id = '', origin = '', title = '', sequence = '',
result_info = '', reasoning = {}, final_result = [])
***************
*** 74,79 ****
@raw = ''
end
- attr_accessor :entry_id, :origin, :title, :sequence,
- :result_info, :reasoning,:final_result, :raw
--- 97,100 ----
***************
*** 83,89 ****
! # Bio::PSORT::PSORT2
class PSORT2
SclNames = {
'csk' => 'cytoskeletal',
--- 104,111 ----
!
class PSORT2
+ # Subcellular localization name codes used by PSORT2
SclNames = {
'csk' => 'cytoskeletal',
***************
*** 101,104 ****
--- 123,127 ----
}
+ # Feature name codes
Features = [
'psg', # PSG: PSG score
***************
*** 139,142 ****
--- 162,166 ----
]
+ # Feature name codes (long version).
FeaturesLong = {
'psg' => 'PSG',
***************
*** 176,185 ****
}
! # Bio::PSORT::PSORT2::Report
class Report
BOUNDARY = '-' * 75
RS = DELIMITER = "\)\n\n#{BOUNDARY}"
def initialize(raw = '', entry_id = nil, scl = nil, definition = nil,
seq = nil, k = nil, features = {}, prob = {}, pred = nil)
--- 200,244 ----
}
! # = Bio::PSORT::PSORT2::Report
! # Report parser classe for PSORT II(PSORT2).
! # == Example
class Report
+ # Report boundary string.
BOUNDARY = '-' * 75
+
+
+ # Report delimiter.
RS = DELIMITER = "\)\n\n#{BOUNDARY}"
+ # entry_id of query sequence.
+ attr_accessor :entry_id
+
+ # Given subcellular localization (three letters code).
+ attr_accessor :scl
+
+ # Definition of query sequence.
+ attr_accessor :definition
+
+ # Sequence of query sequence.
+ attr_accessor :seq
+
+ # k parameter of k-nearest neighbors classifier.
+ attr_accessor :k
+
+ # Feature vector used the kNN prediction.
+ attr_accessor :features
+
+ # Probability vector of kNN prediction.
+ attr_accessor :prob
+
+ # Predicted subcellular localization (three letters code).
+ attr_accessor :pred
+
+ # Raw text of output report.
+ attr_accessor :raw
+
+
+ # Constructs aBio::PSORT::PSORT2::Report object.
def initialize(raw = '', entry_id = nil, scl = nil, definition = nil,
seq = nil, k = nil, features = {}, prob = {}, pred = nil)
***************
*** 194,202 ****
@raw = raw
end
- attr_accessor :entry_id, :scl, :definition, :seq,
- :k, :features, :prob, :pred, :raw
! # report format to be auto detection
def self.parser(str, entry_id)
case str
--- 253,259 ----
@raw = raw
end
! # Parses output report with output format detection automatically.
def self.parser(str, entry_id)
case str
***************
*** 214,219 ****
end
!
! # $id: too short length ($leng), skipped\n";
def self.too_short_parser(ent, entry_id = nil)
report = self.new(ent)
--- 271,277 ----
end
! # Parser for ``too short length'' report.
! #
! # $id: too short length ($leng), skipped\n";
def self.too_short_parser(ent, entry_id = nil)
report = self.new(ent)
***************
*** 227,232 ****
! # default report
! # ``psort test.faa'' output
def self.default_parser(ent, entry_id = nil)
report = self.new(ent, entry_id)
--- 285,290 ----
! # Parser for the default report format.
! # ``psort report'' output.
def self.default_parser(ent, entry_id = nil)
report = self.new(ent, entry_id)
***************
*** 247,251 ****
end
!
def set_header_line(str)
str.sub!(/^-+\n/,'')
--- 305,309 ----
end
! # Returns header information.
def set_header_line(str)
str.sub!(/^-+\n/,'')
***************
*** 264,268 ****
end
!
def self.set_kNN_prob(str)
prob = Hash.new
--- 322,326 ----
end
! # Returns @prob value.
def self.set_kNN_prob(str)
prob = Hash.new
***************
*** 278,282 ****
end
!
def set_prediction(str)
case str
--- 336,340 ----
end
! # Returns @prob and @k values.
def set_prediction(str)
case str
***************
*** 292,297 ****
!
! # ``psort -v report'' and WWW server output
def self.v_parser(ent, entry_id = nil)
report = Bio::PSORT::PSORT2::Report.new(ent, entry_id)
--- 350,355 ----
! # Parser for the verbose output report format.
! # ``psort -v report'' and WWW server output.
def self.v_parser(ent, entry_id = nil)
report = Bio::PSORT::PSORT2::Report.new(ent, entry_id)
***************
*** 304,308 ****
ent[i] = nil
end
! if /^none/ =~ e # for psort output bug
j = self.__send__(:search_j, i, ent)
ent[i - j] += e
--- 362,366 ----
ent[i] = nil
end
! if /^none/ =~ e # psort output bug
j = self.__send__(:search_j, i, ent)
ent[i - j] += e
***************
*** 311,315 ****
}
ent.compact!
- # ent.each_with_index {|e,i| p [i.to_s.ljust(2), e] }
if /^ PSORT II server/ =~ ent[0] # for WWW version
--- 369,372 ----
***************
*** 334,337 ****
--- 391,395 ----
+ #
def self.search_j(i, ent)
j = 1
***************
*** 347,359 ****
! # divide entry body
! def self.divent(ent)
! boundary = ent.index(BOUNDARY)
return ent[0..(boundary - 1)], ent[(boundary + 2)..ent.length]
end
!
! def set_features(fary)
! fary.each {|fent|
key = fent.split(/\:( |\n)/)[0].strip
self.features[key] = fent # unless /^\>/ =~ key
--- 405,417 ----
! # Divides entry body
! def self.divent(entry)
! boundary = entry.index(BOUNDARY)
return ent[0..(boundary - 1)], ent[(boundary + 2)..ent.length]
end
! # Sets @features values.
! def set_features(features_ary)
! features_ary.each {|fent|
key = fent.split(/\:( |\n)/)[0].strip
self.features[key] = fent # unless /^\>/ =~ key
***************
*** 414,479 ****
end
-
-
-
-
-
- =begin
-
- = Bio::PSORT::PSORT1
-
- = Bio::PSORT::PSORT1::Report
-
- --- Bio::PSORT::PSORT1::Report.parser
- --- Bio::PSORT::PSORT1::Report#entry_id
- --- Bio::PSORT::PSORT1::Report#origin
- --- Bio::PSORT::PSORT1::Report#title
- --- Bio::PSORT::PSORT1::Report#sequence
- --- Bio::PSORT::PSORT1::Report#result_info
- --- Bio::PSORT::PSORT1::Report#reasoning
- --- Bio::PSORT::PSORT1::Report#final_result
- --- Bio::PSORT::PSORT1::Report#raw
-
-
-
-
-
- = Bio::PSORT::PSORT2
-
- --- Bio::PSORT::SclNames
- --- Bio::PSORT::Features
- --- Bio::PSORT::FeaturesLong
-
- = Bio::PSORT::PSORT2::Report
-
- Parsed results of the PSORT2 report for default, ``-v'' and WWW version
- output format.
-
- --- Bio::PSORT::PSORT2::Report.new
- --- Bio::PSORT::PSORT2::Report#entry_id
-
-
- --- Bio::PSORT::PSORT2::Report#scl
- --- Bio::PSORT::PSORT2::Report#definition
- --- Bio::PSORT::PSORT2::Report#seq
- --- Bio::PSORT::PSORT2::Report#features
- --- Bio::PSORT::PSORT2::Report#prob
- --- Bio::PSORT::PSORT2::Report#pred
- --- Bio::PSORT::PSORT2::Report#k
- --- Bio::PSORT::PSORT2::Report#raw
-
-
- --- Bio::PSORT::PSORT2::Report.parser(report)
-
- Returns a PSORT report object (Bio::PSORT::PSORT2::Report).
- Formats are auto detedted.
-
- --- Bio::PSORT::PSORT2::Report::BOUNDARY
-
- Fields boundary in a PSORT report.
-
- --- Bio::PSORT::PSORT2::Report::DELIMITER
-
- Entry boundary in PSORT reports.
-
- =end
--- 472,473 ----
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