bio 1.4.2 → 1.4.3

data/lib/bio/data/na.rb

@@ -162,7 +162,7 @@ class NucleicAcid
         'y' => '[tcy]',
         'r' => '[agr]',
         'w' => '[atw]',
-        's' => '[gcw]',
+        's' => '[gcs]',
         'k' => '[tgk]',
         'm' => '[acm]',
         'b' => '[tgcyskb]',

data/lib/bio/db/embl/embl.rb

@@ -196,53 +196,127 @@ class EMBL < EMBLDB
 
 
 
+  #--
   ##
   # DE Line; description (>=1)
   #
+  #++
 
 
+  #--
   ##
   # KW Line; keyword (>=1)
   # KW   [Keyword;]+
   #
   # Bio::EMBLDB#kw  -> Array
   #            #keywords  -> Array
+  #++
 
 
+  #--
   ##
   # OS Line; organism species (>=1)
   # OS   Genus species (name)
   # "OS   Trifolium repens (white clover)"
   #
   # Bio::EMBLDB#os  -> Array
+  #++
 
+  # returns contents in the OS line.
+  # * Bio::EMBL#os  -> Array of <OS Hash>
+  # where <OS Hash> is:
+  #  [{'name'=>'Human', 'os'=>'Homo sapiens'}, 
+  #   {'name'=>'Rat', 'os'=>'Rattus norveticus'}]
+  # * Bio::EMBL#os[0]['name'] => "Human"
+  # * Bio::EMBL#os[0] => {'name'=>"Human", 'os'=>'Homo sapiens'}
+  #--
+  # * Bio::EMBL#os(0) => "Homo sapiens (Human)"
+  #++
+  #
+  # OS Line; organism species (>=1)
+  #   OS   Trifolium repens (white clover)
+  #
+  # Typically, OS line shows "Genus species (name)" style:
+  #   OS   Genus species (name)
+  #
+  # Other examples:
+  #   OS   uncultured bacterium
+  #   OS   xxxxxx metagenome
+  #   OS   Cloning vector xxxxxxxx
+  # Complicated examples:
+  #   OS   Poeciliopsis gracilis (Poeciliopsis gracilis (Heckel, 1848))
+  #   OS   Etmopterus sp. B Last & Stevens, 1994 (bristled lanternshark)
+  #   OS   Galaxias sp. D (Allibone et al., 1996) (Pool Burn galaxias)
+  #   OS   Sicydiinae sp. 'Keith et al., 2010'
+  #   OS   Acanthopagrus sp. 'Jean & Lee, 2008'
+  #   OS   Gaussia princeps (T. Scott, 1894)
+  #   OS   Rana sp. 8 Hillis & Wilcox, 2005
+  #   OS   Contracaecum rudolphii C D'Amelio et al., 2007
+  #   OS   Partula sp. 'Mt. Marau, Tahiti'
+  #   OS   Leptocephalus sp. 'type II larva' (Smith, 1989)
+  #   OS   Tayloria grandis (D.G.Long) Goffinet & A.J.Shaw, 2002
+  #   OS   Non-A, non-B hepatitis virus
+  #   OS   Canidae (dog, coyote, wolf, fox)
+  #   OS   Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
+  #   OS   Yersinia enterocolitica (type O:5,27)
+  #   OS   Influenza A virus (A/green-winged teal/OH/72/99(H6N1,4))
+  #   OS   Influenza A virus (A/Beijing/352/1989,(highgrowth reassortant NIB26)(H3N2))
+  #   OS   Recombinant Hepatitis C virus H77(5'UTR-NS2)/JFH1_V787A,Q1247L
+  #
+  def os(num = nil)
+    unless @data['OS']
+      os = Array.new
+      tmp = fetch('OS')
+      if /([A-Z][a-z]* *[\w\d \:\'\+\-]+[\w\d]) *\(([\w\d ]+)\)\s*\z/ =~ tmp
+        org = $1
+        os.push({'name' => $2, 'os' => $1})
+      else
+        os.push({'name' => nil, 'os' => tmp})
+      end
+      @data['OS'] = os
+    end
+    if num
+      # EX. "Trifolium repens (white clover)"
+      "#{@data['OS'][num]['os']} {#data['OS'][num]['name']"
+    end
+    @data['OS']
+  end
 
+
+  #--
   ##
   # OC Line; organism classification (>=1)
   #
   # Bio::EMBLDB#oc  -> Array
+  #++
 
 
+  #--
   ##
   # OG Line; organella (0 or 1/entry)
   # ["Mitochondrion", "Chloroplast","Kinetoplast", "Cyanelle", "Plastid"]
   #  or a plasmid name (e.g. "Plasmid pBR322").  
   #
   # Bio::EMBLDB#og  -> String
+  #++
 
 
+  #--
   ##
   # R Lines
   # RN RC RP RX RA RT RL
   #
   # Bio::EMBLDB#ref
+  #++
   
   
+  #--
   ##
   # DR Line; defabases cross-regerence (>=0)
   # "DR  database_identifier; primary_identifier; secondary_identifier."
   #
   # Bio::EMBLDB#dr
+  #++
 
 
   # returns feature table header (String) in the feature header (FH) line.

data/lib/bio/db/embl/format_embl.rb

@@ -6,10 +6,6 @@
 #              Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: format_embl.rb,v 1.1.2.7 2008/06/19 12:45:15 ngoto Exp $
-#
-
-require 'bio/sequence/format'
 
 module Bio::Sequence::Format::NucFormatter
 

data/lib/bio/db/fasta.rb

@@ -35,7 +35,7 @@ module Bio
 
   # Treats a FASTA formatted entry, such as:
   #
-  #   >id and/or some comments                    <== comment line
+  #   >id and/or some comments                    <== definition line
   #   ATGCATGCATGCATGCATGCATGCATGCATGCATGC        <== sequence lines
   #   ATGCATGCATGCATGCATGCATGCATGCATGCATGC
   #   ATGCATGCATGC
@@ -45,52 +45,64 @@ module Bio
   #
   # === Examples
   #
-  #   f_str = <<END_OF_STRING
-  #   >sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
-  #   MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
-  #   VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
-  #   GIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL
-  #   KLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC
-  #   IFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP
-  #   QWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES
-  #   >sce:YBR274W  CHK1; probable serine/threonine-protein kinase [EC:2.7.1.-] [SP:KB9S_YEAST]
-  #   MSLSQVSPLPHIKDVVLGDTVGQGAFACVKNAHLQMDPSIILAVKFIHVP
-  #   TCKKMGLSDKDITKEVVLQSKCSKHPNVLRLIDCNVSKEYMWIILEMADG
-  #   GDLFDKIEPDVGVDSDVAQFYFQQLVSAINYLHVECGVAHRDIKPENILL
-  #   DKNGNLKLADFGLASQFRRKDGTLRVSMDQRGSPPYMAPEVLYSEEGYYA
-  #   DRTDIWSIGILLFVLLTGQTPWELPSLENEDFVFFIENDGNLNWGPWSKI
-  #   EFTHLNLLRKILQPDPNKRVTLKALKLHPWVLRRASFSGDDGLCNDPELL
-  #   AKKLFSHLKVSLSNENYLKFTQDTNSNNRYISTQPIGNELAELEHDSMHF
-  #   QTVSNTQRAFTSYDSNTNYNSGTGMTQEAKWTQFISYDIAALQFHSDEND
-  #   CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
-  #   FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
-  #   KTGDPLEWRRLFKKISTICRDIILIPN
+  #   fasta_string = <<END_OF_STRING
+  #   >gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c]
+  #   MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNI
+  #   VRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQ
+  #   NLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKP
+  #   IFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDP
+  #   INRISARRAAIHPYFQES
   #   END_OF_STRING
   #
-  #   f = Bio::FastaFormat.new(f_str)
-  #   puts "### FastaFormat"
-  #   puts "# entry"
-  #   puts f.entry
-  #   puts "# entry_id"
-  #   p f.entry_id
-  #   puts "# definition"
-  #   p f.definition
-  #   puts "# data"
-  #   p f.data
-  #   puts "# seq"
-  #   p f.seq
-  #   puts "# seq.type"
-  #   p f.seq.type
-  #   puts "# length"
-  #   p f.length
-  #   puts "# aaseq"
-  #   p f.aaseq
-  #   puts "# aaseq.type"
-  #   p f.aaseq.type
-  #   puts "# aaseq.composition"
-  #   p f.aaseq.composition
-  #   puts "# aalen"
-  #   p f.aalen
+  #   f = Bio::FastaFormat.new(fasta_string)
+  #   
+  #   f.entry #=> ">gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c]\n"+
+  #   # MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNI\n"+
+  #   # VRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQ\n"+
+  #   # NLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKP\n"+
+  #   # IFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDP\n"+
+  #   # INRISARRAAIHPYFQES"
+  #   
+  # ==== Methods related to the name of the sequence
+  # 
+  # A larger range of methods for dealing with Fasta definition lines can be found in FastaDefline, accessed through the FastaFormat#identifiers method.
+  # 
+  #   f.entry_id #=> "gi|398365175"
+  #   f.definition #=> "gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c]"
+  #   f.identifiers #=> Bio::FastaDefline instance
+  #   f.accession #=> "NP_009718"
+  #   f.accessions #=> ["NP_009718"]
+  #   f.acc_version #=> "NP_009718.3"
+  #   f.comment #=> nil
+  #   
+  # ==== Methods related to the actual sequence
+  #
+  #   f.seq #=> "MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES"
+  #   f.data #=> "\nMSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNI\nVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQ\nNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKP\nIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDP\nINRISARRAAIHPYFQES\n"
+  #   f.length #=> 298
+  #   f.aaseq #=> "MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES"
+  #   f.aaseq.composition #=> {"M"=>5, "S"=>15, "G"=>21, "E"=>16, "L"=>36, "A"=>17, "N"=>8, "Y"=>13, "K"=>22, "R"=>20, "V"=>18, "T"=>7, "D"=>23, "P"=>17, "Q"=>10, "I"=>23, "H"=>7, "F"=>12, "C"=>4, "W"=>4}
+  #   f.aalen #=> 298
+  #
+  #
+  # === A less structured fasta entry
+  #
+  #   f.entry #=> ">abc 123 456\nASDF"
+  #
+  #   f.entry_id #=> "abc"
+  #   f.definition #=> "abc 123 456"
+  #   f.comment #=> nil
+  #   f.accession #=> nil
+  #   f.accessions #=> []
+  #   f.acc_version #=> nil
+  #
+  #   f.seq #=> "ASDF"
+  #   f.data #=> "\nASDF\n"
+  #   f.length #=> 4
+  #   f.aaseq #=> "ASDF"
+  #   f.aaseq.composition #=> {"A"=>1, "S"=>1, "D"=>1, "F"=>1}
+  #   f.aalen #=> 4
+  #
   #
   # === References
   #

data/lib/bio/db/fasta/defline.rb

@@ -120,7 +120,7 @@ module Bio
   #      ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
   #      ["gb", "AAB29504.1", nil], ["Cavia"]]
   #
-  # === Refereneces
+  # === References
   #
   # * Fasta format description (NCBI)
   #   http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml

data/lib/bio/db/fasta/format_fasta.rb

@@ -7,10 +7,6 @@
 #               Jan Aerts <jan.aerts@bbsrc.ac.uk>
 # License::    The Ruby License
 #
-# $Id: format_fasta.rb,v 1.1.2.1 2008/03/04 11:26:59 ngoto Exp $
-#
-
-require 'bio/sequence/format'
 
 module Bio::Sequence::Format::Formatter
 

data/lib/bio/db/fasta/format_qual.rb

@@ -5,11 +5,6 @@
 #               Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
-#
-
-require 'bio/sequence/format'
-require 'bio/sequence/quality_score'
 
 module Bio::Sequence::Format::Formatter
 

data/lib/bio/db/fastq/format_fastq.rb

@@ -7,7 +7,6 @@
 #
 
 require 'bio/db/fastq'
-require 'bio/sequence/format'
 
 module Bio::Sequence::Format::Formatter
 

data/lib/bio/db/genbank/format_genbank.rb

@@ -4,10 +4,6 @@
 # Copyright::  Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: format_genbank.rb,v 1.1.2.5 2008/06/17 15:59:24 ngoto Exp $
-#
-
-require 'bio/sequence/format'
 
 module Bio::Sequence::Format::NucFormatter
 

data/lib/bio/db/gff.rb

@@ -454,7 +454,8 @@ module Bio
 
         # Return the record as a GFF2 compatible string
         def to_s
-          cmnt = if @comment and !@comment.to_s.strip.empty? then
+          cmnt = if defined?(@comment) and @comment and
+                     !@comment.to_s.strip.empty? then
                    @comment.gsub(/[\r\n]+/, ' ')
                  else
                    false
@@ -996,21 +997,46 @@ module Bio
           str.empty? ? '.' : str
         end
 
+        if URI.const_defined?(:Parser) then
+          # (private) URI::Parser object for escape/unescape GFF3 columns
+          URI_PARSER = URI::Parser.new
+
+          # (private) the same as URI::Parser#escape(str, unsafe)
+          def _escape(str, unsafe)
+            URI_PARSER.escape(str, unsafe)
+          end
+
+          # (private) the same as URI::Parser#unescape(str)
+          def _unescape(str)
+            URI_PARSER.unescape(str)
+          end
+        else
+          # (private) the same as URI.escape(str, unsafe)
+          def _escape(str, unsafe)
+            URI.escape(str, unsafe)
+          end
+
+          # (private) the same as URI.unescape(str)
+          def _unescape(str)
+            URI.unescape(str)
+          end
+        end
+
         # Return the string corresponding to these characters unescaped
         def unescape(string)
-          URI.unescape(string)
+          _unescape(string)
         end
 
         # Escape a column according to the specification at
         # http://song.sourceforge.net/gff3.shtml.
         def escape(string)
-          URI.escape(string, UNSAFE)
+          _escape(string, UNSAFE)
         end
 
         # Escape seqid column according to the specification at
         # http://song.sourceforge.net/gff3.shtml.
         def escape_seqid(string)
-          URI.escape(string, UNSAFE_SEQID)
+          _escape(string, UNSAFE_SEQID)
         end
         
         # Escape attribute according to the specification at
@@ -1019,7 +1045,7 @@ module Bio
         # are escaped: ",=;".
         # Returns the string corresponding to these characters escaped.
         def escape_attribute(string)
-          URI.escape(string, UNSAFE_ATTRIBUTE)
+          _escape(string, UNSAFE_ATTRIBUTE)
         end
       end #module Escape
 
@@ -1028,6 +1054,7 @@ module Bio
       # Stores meta-data "##sequence-region seqid start end".
       class SequenceRegion
         include Escape
+        extend Escape
         
         # creates a new SequenceRegion class
         def initialize(seqid, start, endpos)
@@ -1039,7 +1066,7 @@ module Bio
         # parses given string and returns SequenceRegion class
         def self.parse(str)
           dummy, seqid, start, endpos =
-            str.chomp.split(/\s+/, 4).collect { |x| URI.unescape(x) }
+            str.chomp.split(/\s+/, 4).collect { |x| unescape(x) }
           self.new(seqid, start, endpos)
         end
 
@@ -1139,7 +1166,8 @@ module Bio
 
         # Return the record as a GFF3 compatible string
         def to_s
-          cmnt = if @comment and !@comment.to_s.strip.empty? then
+          cmnt = if defined?(@comment) and @comment and
+                     !@comment.to_s.strip.empty? then
                    @comment.gsub(/[\r\n]+/, ' ')
                  else
                    false
@@ -1163,6 +1191,7 @@ module Bio
         # data of "Target" attribute.
         class Target
           include GFF3::Escape
+          extend GFF3::Escape
 
           # Creates a new Target object.
           def initialize(target_id, start, endpos, strand = nil)
@@ -1190,7 +1219,7 @@ module Bio
           #
           def self.parse(str)
             target_id, start, endpos, strand =
-              str.split(/ +/, 4).collect { |x| URI.unescape(x) }
+              str.split(/ +/, 4).collect { |x| unescape(x) }
             self.new(target_id, start, endpos, strand)
           end
 
@@ -1332,15 +1361,15 @@ module Bio
 
             # rest of data_ref
             len = 0
-            data_ref.each do |ref|
-              len += ref.length if ref.code == :M
+            data_ref.each do |r|
+              len += r.length if r.code == :M
             end
             data.push Code.new(:D, len) if len > 0
 
             # rest of data_tgt
             len = 0
-            data_tgt.each do |tgt|
-              len += tgt.length if tgt.code == :M
+            data_tgt.each do |t|
+              len += t.length if t.code == :M
             end
             data.push Code.new(:I, len) if len > 0