[BioRuby-cvs] bioruby/lib/bio/appl/genscan report.rb,1.6,1.7
Mitsuteru C. Nakao
nakao at pub.open-bio.org
Sun Nov 6 13:24:43 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/appl/genscan
In directory pub.open-bio.org:/tmp/cvs-serv14390/lib/bio/appl/genscan
Modified Files:
report.rb
Log Message:
* Converted to RDoc.
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/genscan/report.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** report.rb 1 Nov 2005 05:15:15 -0000 1.6
--- report.rb 6 Nov 2005 18:24:41 -0000 1.7
***************
*** 1,6 ****
#
! # bio/appl/genscan/report.rb - Genscan report classes
#
! # Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
#
# This library is free software; you can redistribute it and/or
--- 1,17 ----
#
! # = bio/appl/genscan/report.rb - Genscan report classes
#
! # Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # Licence:: LGPL
! #
! # $Id$
! #
! # == Description
! #
! #
! # == Example
! # == References
! #
! #--
#
# This library is free software; you can redistribute it and/or
***************
*** 20,23 ****
--- 31,36 ----
# $Id$
#
+ #++
+ #
require 'bio/db/fasta'
***************
*** 26,45 ****
module Bio
! # Bio::Genscan
class Genscan
! # Bio::Genscan::Report - Class for Genscan report output.
class Report
attr_reader :genscan_version
attr_reader :date_run
attr_reader :time
attr_reader :query_name
alias_method :sequence_name, :query_name
alias_method :name, :query_name
attr_reader :length
attr_reader :gccontent
attr_reader :isochore
attr_reader :matrix
attr_reader :predictions
alias_method :prediction, :predictions
--- 39,78 ----
module Bio
! # = Bio::Genscan
class Genscan
! # = Bio::Genscan::Report - Class for Genscan report output.
! #
! # Parser for the Genscan report output.
! # * Genscan http://genes.mit.edu/GENSCAN.html
class Report
+ # Returns Genscan version.
attr_reader :genscan_version
+
+ # Returns
attr_reader :date_run
+
+ # Returns
attr_reader :time
+
+ # Returns Name of query sequence.
attr_reader :query_name
alias_method :sequence_name, :query_name
alias_method :name, :query_name
+
+ # Returns Length of the query sequence.
attr_reader :length
+
+ # Returns C+G content of the query sequence.
attr_reader :gccontent
+
+ # Returns
attr_reader :isochore
+
+ # Returns
attr_reader :matrix
+
+ # Returns Array of Bio::Genscan::Report::Gene.
attr_reader :predictions
alias_method :prediction, :predictions
***************
*** 177,181 ****
! # Bio::Genescan::Report::Gene
class Gene
--- 210,214 ----
! # = Container class of predicted gene structures.
class Gene
***************
*** 189,197 ****
--- 222,242 ----
@polyA = nil
end
+
+ # Returns "Gn", gene number field.
attr_reader :number
+
+ # Returns Bio::FastaFormat object.
attr_reader :aaseq
+
+ # Returns Bio::FastaFormat object.
attr_reader :naseq
+
+ # Returns Array of Bio::Genscan::Report::Exon.
attr_reader :exons
+
+ # Returns Bio::Genscan::Report::Exon object.
attr_reader :promoter
+
+ # Returns Bio::Genscan::Report::Exon object.
attr_reader :polyA
***************
*** 223,229 ****
! # Bio::Genescan::Report::Exon
class Exon
# Bio::Genescan::Report::Exon.parser
def self.parser(line)
--- 268,285 ----
! # = Container class of a predicted gene structure.
class Exon
+ #
+ TYPES = {
+ 'Init' => 'Initial exon',
+ 'Intr' => 'Internal exon',
+ 'Term' => 'Terminal exon',
+ 'Sngl' => 'Single-exon gene',
+ 'Prom' => 'Promoter',
+ 'PlyA' => 'poly-A signal'
+ }
+
+
# Bio::Genescan::Report::Exon.parser
def self.parser(line)
***************
*** 239,253 ****
end
-
- TYPES = {
- 'Init' => 'Initial exon',
- 'Intr' => 'Internal exon',
- 'Term' => 'Terminal exon',
- 'Sngl' => 'Single-exon gene',
- 'Prom' => 'Promoter',
- 'PlyA' => 'poly-A signal'
- }
# Bio::Genescan::Report::Exon.new(gene_number, exon_type, strand, first,
# end, length, frame, phase, acceptor_score, donor_score, score, p_value,
--- 295,334 ----
end
+ # Returns
+ attr_reader :gene_number
+
+ # Returns "Ex", exon number field
+ attr_reader :number
+
+ # Returns "Type" field.
+ attr_reader :exon_type
+
+ # Returns "S" field.
+ attr_reader :strand
+
+ # Returns Returns first position of the region. "Begin" field.
+ attr_reader :first
+
+ # Returns Returns last position of the region. "End" field.
+ attr_reader :last
+
+ # Returns "Fr" field.
+ attr_reader :frame
+
+ # Returns "Ph" field.
+ attr_reader :phase
+
+ # Returns "CodRg" field.
+ attr_reader :score
+ # Returns "P" field.
+ attr_reader :p_value
+
+ # Returns "Tscr" field.
+ attr_reader :t_score
+ alias_method :coding_region_score, :score
+
+
# Bio::Genescan::Report::Exon.new(gene_number, exon_type, strand, first,
# end, length, frame, phase, acceptor_score, donor_score, score, p_value,
***************
*** 268,286 ****
@t_score = ts.to_f
end
! attr_reader :gene_number
! attr_reader :number
! attr_reader :exon_type
! attr_reader :strand
! attr_reader :first
! attr_reader :last
! attr_reader :frame
! attr_reader :phase
! attr_reader :score
! attr_reader :p_value
! attr_reader :t_score
! alias_method :coding_region_score, :score
# Bio::Genescan::Report::Exon#exon_type_long
def exon_type_long
TYPES[exon_type]
--- 349,358 ----
@t_score = ts.to_f
end
!
# Bio::Genescan::Report::Exon#exon_type_long
+ #
+ # Returns a human-readable "Type" of exon.
def exon_type_long
TYPES[exon_type]
***************
*** 289,292 ****
--- 361,366 ----
# Bio::Genescan::Report::Exon#range
+ #
+ # Returns Range object of the region.
def range
Range.new(@first, @last)
***************
*** 295,298 ****
--- 369,374 ----
# Bio::Genescan::Report::Exon#acceptor_score
+ #
+ # "I/Ac" field.
def acceptor_score
@i_ac
***************
*** 302,305 ****
--- 378,383 ----
# Bio::Genescan::Report::Exon#donor_score
+ #
+ # "Do/T" field.
def donor_score
@do_t
***************
*** 421,556 ****
=begin
-
- = Bio::Genscan::Report
-
- Parser for the Genscan report output.
- * ((Genscan|URL:http://genes.mit.edu/GENSCAN.html)
-
-
- --- Bio::Genscan::Report.new(report)
-
- Parse a Genscan report output.
-
- --- Bio::Genscan::Report#genscan_version
-
- Genscan version.
-
- --- Bio::Genscan::Report#date_run
- --- Bio::Genscan::Report#time
- --- Bio::Genscan::Report#query_name
-
- Name of query sequence.
-
- --- Bio::Genscan::Report#length
-
- Length of the query sequence.
-
- --- Bio::Genscan::Report#gccontent
-
- C+G content of the query sequence.
-
- --- Bio::Genscan::Report#isochore
- --- Bio::Genscan::Report#predictions
-
- Array of Bio::Genscan::Report::Gene.
-
-
- = Bio::Genscan::Report::Gene
-
- Container class of predicted gene structures.
-
- --- Bio::Genscan::Report::Gene#number
-
- "Gn", gene number field.
-
- --- Bio::Genscan::Report::Gene#aaseq
-
- Returns Bio::FastaFormat object.
-
- --- Bio::Genscan::Report::Gene#naseq
-
- Returns Bio::FastaFormat object.
-
- --- Bio::Genscan::Report::Gene#promoter
-
- Returns Bio::Genscan::Report::Exon object.
-
- --- Bio::Genscan::Report::Gene#polyA
-
- Returns Bio::Genscan::Report::Exon object.
-
- --- Bio::Genscan::Report::Gene#exons
-
- Array of Bio::Genscan::Report::Exon.
-
-
- = Bio::Genscan::Report::Exon
-
- Container class of a predicted gene structure.
-
- --- Bio::Genscan::Report::Gene#number
-
- "Ex", exon number field
-
- --- Bio::Genscan::Report::Gene#exon_type
-
- "Type" field.
-
- --- Bio::Genscan::Report::Gene#exon_type_long
-
- Returns a human-readable "Type" of exon.
-
- --- Bio::Genscan::Report::Gene#strand
-
- "S" field.
-
- --- Bio::Genscan::Report::Gene#first
-
- Returns first position of the region. "Begin" field.
-
- --- Bio::Genscan::Report::Gene#last
-
- Returns last position of the region. "End" field.
-
- --- Bio::Genscan::Report::Gene#range
-
- Returns Range object of the region.
-
- --- Bio::Genscan::Report::Gene#frame
-
- "Fr" field.
-
- --- Bio::Genscan::Report::Gene#phase
-
- "Ph" field.
-
- --- Bio::Genscan::Report::Gene#acceptor_score
-
- "I/Ac" field.
-
- --- Bio::Genscan::Report::Gene#donor_score
-
- "Do/T" field.
-
- --- Bio::Genscan::Report::Gene#initiation_score
-
- "I/Ac" field.
-
- --- Bio::Genscan::Report::Gene#termination_score
-
- "Do/T" field.
-
- --- Bio::Genscan::Report::Gene#score
-
- "CodRg" field.
-
- --- Bio::Genscan::Report::Gene#p_value
-
- "P" field.
-
- --- Bio::Genscan::Report::Gene#t_score
-
- "Tscr" field.
-
--- 499,502 ----
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