[BioRuby-cvs] bioruby/lib/bio/db/embl common.rb, 1.8, 1.9 embl.rb, 1.25, 1.26 sptr.rb, 1.29, 1.30 swissprot.rb, 1.3, 1.4 trembl.rb, 1.3, 1.4 uniprot.rb, 1.1, 1.2
Mitsuteru C. Nakao
nakao at pub.open-bio.org
Sat Jan 28 06:40:41 UTC 2006
Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory pub.open-bio.org:/tmp/cvs-serv4726/lib/bio/db/embl
Modified Files:
common.rb embl.rb sptr.rb swissprot.rb trembl.rb uniprot.rb
Log Message:
* Updated RDoc.
Index: sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** sptr.rb 2 Nov 2005 07:30:14 -0000 1.29
--- sptr.rb 28 Jan 2006 06:40:38 -0000 1.30
***************
*** 7,15 ****
# $Id$
#
! # == UniProtKB/SwissProt and TrEMBL
#
! # See the SWISS-PROT dicument file SPECLIST.TXT.
#
! # == Example
#
#--
--- 7,34 ----
# $Id$
#
! # == Description
! #
! # Shared methods for UniProtKB/SwissProt and TrEMBL classes.
#
! # See the SWISS-PROT document file SPECLIST.TXT or UniProtKB/SwissProt
! # user manual.
! #
! # == Examples
#
! # str = File.read("p53_human.swiss")
! # obj = Bio::SPTR.new(str)
! # obj.entry_id #=> "P53_HUMAN"
! #
! # == References
! #
! # * Swiss-Prot Protein knowledgebase. TrEMBL Computer-annotated supplement
! # to Swiss-Prot
! # http://au.expasy.org/sprot/
! #
! # * UniProt
! # http://uniprot.org/
! #
! # * The UniProtKB/SwissProt/TrEMBL User Manual
! # http://www.expasy.org/sprot/userman.html
#
#--
***************
*** 37,41 ****
module Bio
! # Parser class for UniProtKB/SwissProt and TrEMBL database entry
class SPTR < EMBLDB
include Bio::EMBLDB::Common
--- 56,60 ----
module Bio
! # Parser class for UniProtKB/SwissProt and TrEMBL database entry.
class SPTR < EMBLDB
include Bio::EMBLDB::Common
***************
*** 46,60 ****
# returns a Hash of the ID line.
# returns a content (Int or String) of the ID line by a given key.
# Hash keys: ['ENTRY_NAME', 'DATA_CLASS', 'MODECULE_TYPE', 'SEQUENCE_LENGTH']
#
! # ID Line
! # "ID #{ENTRY_NAME} #{DATA_CLASS}; #{MOLECULE_TYPE}; #{SEQUENCE_LENGTH}."
#
- # ENTRY_NAME := "#{X}_#{Y}"
- # X =~ /[A-Z0-9]{1,5}/ # The protein name.
- # Y =~ /[A-Z0-9]{1,5}/ # The biological source of the protein.
- # MOLECULE_TYPE := 'PRT' =~ /\w{3}/
- # SEQUENCE_LENGTH =~ /\d+ AA/
def id_line(key = nil)
unless @data['ID']
--- 65,81 ----
# returns a Hash of the ID line.
+ #
# returns a content (Int or String) of the ID line by a given key.
# Hash keys: ['ENTRY_NAME', 'DATA_CLASS', 'MODECULE_TYPE', 'SEQUENCE_LENGTH']
#
! # === ID Line
! # ID P53_HUMAN STANDARD; PRT; 393 AA.
! # #"ID #{ENTRY_NAME} #{DATA_CLASS}; #{MOLECULE_TYPE}; #{SEQUENCE_LENGTH}."
! #
! # === Examples
! # obj.id_line #=> {"ENTRY_NAME"=>"P53_HUMAN", "DATA_CLASS"=>"STANDARD", "SEQUENCE_LENGTH"=>393, "MOLECULE_TYPE"=>"PRT"}
! #
! # obj.id_line('ENTRY_NAME') #=> "P53_HUMAN"
#
def id_line(key = nil)
unless @data['ID']
***************
*** 79,83 ****
# returns a ENTRY_NAME in the ID line.
#
- # A short-cut for Bio::SPTR#id_line('ENTRY_NAME').
def entry_id
id_line('ENTRY_NAME')
--- 100,103 ----
***************
*** 120,127 ****
# returns a String of information in the DT lines by a given key..
#
! # DT Line; date (3/entry)
! # DT DD-MMM-YYY (rel. NN, Created)
! # DT DD-MMM-YYY (rel. NN, Last sequence update)
! # DT DD-MMM-YYY (rel. NN, Last annotation update)
def dt(key = nil)
unless @data['DT']
--- 140,147 ----
# returns a String of information in the DT lines by a given key..
#
! # === DT Line; date (3/entry)
! # DT DD-MMM-YYY (rel. NN, Created)
! # DT DD-MMM-YYY (rel. NN, Last sequence update)
! # DT DD-MMM-YYY (rel. NN, Last annotation update)
def dt(key = nil)
unless @data['DT']
***************
*** 144,148 ****
# returns the proposed official name of the protein.
#
! # DE Line; description (>=1)
# "DE #{OFFICIAL_NAME} (#{SYNONYM})"
# "DE #{OFFICIAL_NAME} (#{SYNONYM}) [CONTEINS: #1; #2]."
--- 164,168 ----
# returns the proposed official name of the protein.
#
! # === DE Line; description (>=1)
# "DE #{OFFICIAL_NAME} (#{SYNONYM})"
# "DE #{OFFICIAL_NAME} (#{SYNONYM}) [CONTEINS: #1; #2]."
***************
*** 193,197 ****
# * Bio::SPTR#gn[0] -> Array # OR
#
! # GN Line: Gene name(s) (>=0, optional)
def gn
return @data['GN'] if @data['GN']
--- 213,217 ----
# * Bio::SPTR#gn[0] -> Array # OR
#
! # === GN Line: Gene name(s) (>=0, optional)
def gn
return @data['GN'] if @data['GN']
***************
*** 206,210 ****
# returns contents in the old style GN line.
! # GN Line: Gene name(s) (>=0, optional)
# GN HNS OR DRDX OR OSMZ OR BGLY.
# GN CECA1 AND CECA2.
--- 226,230 ----
# returns contents in the old style GN line.
! # === GN Line: Gene name(s) (>=0, optional)
# GN HNS OR DRDX OR OSMZ OR BGLY.
# GN CECA1 AND CECA2.
***************
*** 293,297 ****
# * Bio::EPTR#os(0) -> "Homo sapiens (Human)"
#
! # OS Line; organism species (>=1)
# OS Genus species (name).
# OS Genus species (name0) (name1).
--- 313,317 ----
# * Bio::EPTR#os(0) -> "Homo sapiens (Human)"
#
! # === OS Line; organism species (>=1)
# OS Genus species (name).
# OS Genus species (name0) (name1).
***************
*** 338,344 ****
# returns a Hash of oraganism taxonomy cross-references.
# * Bio::SPTR#ox -> Hash
! # {'NCBI_TaxID' => ['1234','2345','3456','4567'], ...}
#
! # OX Line; organism taxonomy cross-reference (>=1 per entry)
# OX NCBI_TaxID=1234;
# OX NCBI_TaxID=1234, 2345, 3456, 4567;
--- 358,364 ----
# returns a Hash of oraganism taxonomy cross-references.
# * Bio::SPTR#ox -> Hash
! # {'NCBI_TaxID' => ['1234','2345','3456','4567'], ...}
#
! # === OX Line; organism taxonomy cross-reference (>=1 per entry)
# OX NCBI_TaxID=1234;
# OX NCBI_TaxID=1234, 2345, 3456, 4567;
***************
*** 369,409 ****
# returns contents in the CC lines.
# * Bio::SPTR#cc -> Hash
!
! # * Bio::SPTR#cc(Int) -> String
! # returns an Array of contents in the TOPIC string.
# * Bio::SPTR#cc(TOPIC) -> Array w/in Hash, Hash
#
# returns contents of the "ALTERNATIVE PRODUCTS".
# * Bio::SPTR#cc('ALTERNATIVE PRODUCTS') -> Hash
! # {'Event' => str,
! # 'Named isoforms' => int,
! # 'Comment' => str,
! # 'Variants'=>[{'Name' => str, 'Synonyms' => str, 'IsoId' => str, 'Sequence' => []}]}
#
! # CC -!- ALTERNATIVE PRODUCTS:
! # CC Event=Alternative splicing; Named isoforms=15;
! # ...
! # CC placentae isoforms. All tissues differentially splice exon 13;
! # CC Name=A; Synonyms=no del;
! # CC IsoId=P15529-1; Sequence=Displayed;
#
# returns contents of the "DATABASE".
# * Bio::SPTR#cc('DATABASE') -> Array
! # [{'NAME'=>str,'NOTE'=>str, 'WWW'=>URI,'FTP'=>URI}, ...]
#
! # CC -!- DATABASE: NAME=Text[; NOTE=Text][; WWW="Address"][; FTP="Address"].
#
# returns contents of the "MASS SPECTROMETRY".
# * Bio::SPTR#cc('MASS SPECTROMETRY') -> Array
! # [{'MW"=>float,'MW_ERR'=>float, 'METHOD'=>str,'RANGE'=>str}, ...]
#
! # MASS SPECTROMETRY: MW=XXX[; MW_ERR=XX][; METHOD=XX][;RANGE=XX-XX].
#
- # CC lines (>=0, optional)
- # CC -!- TISSUE SPECIFICITY: HIGHEST LEVELS FOUND IN TESTIS. ALSO PRESENT
- # CC IN LIVER, KIDNEY, LUNG AND BRAIN.
- #
- # CC -!- TOPIC: FIRST LINE OF A COMMENT BLOCK;
- # CC SECOND AND SUBSEQUENT LINES OF A COMMENT BLOCK.
def cc(tag = nil)
unless @data['CC']
--- 389,429 ----
# returns contents in the CC lines.
# * Bio::SPTR#cc -> Hash
! #
! # returns an object of contents in the TOPIC.
# * Bio::SPTR#cc(TOPIC) -> Array w/in Hash, Hash
#
# returns contents of the "ALTERNATIVE PRODUCTS".
# * Bio::SPTR#cc('ALTERNATIVE PRODUCTS') -> Hash
! # {'Event' => str,
! # 'Named isoforms' => int,
! # 'Comment' => str,
! # 'Variants'=>[{'Name' => str, 'Synonyms' => str, 'IsoId' => str, 'Sequence' => []}]}
#
! # CC -!- ALTERNATIVE PRODUCTS:
! # CC Event=Alternative splicing; Named isoforms=15;
! # ...
! # CC placentae isoforms. All tissues differentially splice exon 13;
! # CC Name=A; Synonyms=no del;
! # CC IsoId=P15529-1; Sequence=Displayed;
#
# returns contents of the "DATABASE".
# * Bio::SPTR#cc('DATABASE') -> Array
! # [{'NAME'=>str,'NOTE'=>str, 'WWW'=>URI,'FTP'=>URI}, ...]
#
! # CC -!- DATABASE: NAME=Text[; NOTE=Text][; WWW="Address"][; FTP="Address"].
#
# returns contents of the "MASS SPECTROMETRY".
# * Bio::SPTR#cc('MASS SPECTROMETRY') -> Array
! # [{'MW"=>float,'MW_ERR'=>float, 'METHOD'=>str,'RANGE'=>str}, ...]
#
! # CC -!- MASS SPECTROMETRY: MW=XXX[; MW_ERR=XX][; METHOD=XX][;RANGE=XX-XX].
! #
! # === CC lines (>=0, optional)
! # CC -!- TISSUE SPECIFICITY: HIGHEST LEVELS FOUND IN TESTIS. ALSO PRESENT
! # CC IN LIVER, KIDNEY, LUNG AND BRAIN.
! #
! # CC -!- TOPIC: FIRST LINE OF A COMMENT BLOCK;
! # CC SECOND AND SUBSEQUENT LINES OF A COMMENT BLOCK.
#
def cc(tag = nil)
unless @data['CC']
***************
*** 542,546 ****
# returns conteins in a line of the CC INTERACTION section.
#
! # CC P46527:CDKN1B; NbExp=1; IntAct=EBI-359815, EBI-519280;
def cc_interaction_parse(str)
it = str.scan(/(.+?); NbExp=(.+?); IntAct=(.+?);/)
--- 562,566 ----
# returns conteins in a line of the CC INTERACTION section.
#
! # CC P46527:CDKN1B; NbExp=1; IntAct=EBI-359815, EBI-519280;
def cc_interaction_parse(str)
it = str.scan(/(.+?); NbExp=(.+?); IntAct=(.+?);/)
***************
*** 556,562 ****
# * Bio::EMBLDB#dr -> Hash w/in Array
#
! # DR Line; defabases cross-reference (>=0)
! # a cross_ref pre one line
! # DR database_identifier; primary_identifier; secondary_identifier.
@@dr_database_identifier = ['EMBL','CARBBANK','DICTYDB','ECO2DBASE',
'ECOGENE',
--- 576,582 ----
# * Bio::EMBLDB#dr -> Hash w/in Array
#
! # === DR Line; defabases cross-reference (>=0)
! # DR database_identifier; primary_identifier; secondary_identifier.
! # a cross_ref pre one line
@@dr_database_identifier = ['EMBL','CARBBANK','DICTYDB','ECO2DBASE',
'ECOGENE',
***************
*** 575,595 ****
# returns conteins in the feature table.
# * Bio::SPTR#ft -> Hash
! # {'feature_name' => [{'From' => str, 'To' => str,
! # 'Description' => str, 'FTId' => str}],...}
#
# returns an Array of the information about the feature_name in the feature table.
# * Bio::SPTR#ft(feature_name) -> Array of Hash
! # [{'From' => str, 'To' => str, 'Description' => str, 'FTId' => str},...]
#
! # FT Line; feature table data (>=0, optional)
#
! # Col Data item
! # ----- -----------------
! # 1- 2 FT
! # 6-13 Feature name
! # 15-20 `FROM' endpoint
! # 22-27 `TO' endpoint
! # 35-75 Description (>=0 per key)
! # ----- -----------------
def ft(feature_name = nil)
unless @data['FT']
--- 595,615 ----
# returns conteins in the feature table.
# * Bio::SPTR#ft -> Hash
! # {'feature_name' => [{'From' => str, 'To' => str,
! # 'Description' => str, 'FTId' => str}],...}
#
# returns an Array of the information about the feature_name in the feature table.
# * Bio::SPTR#ft(feature_name) -> Array of Hash
! # [{'From' => str, 'To' => str, 'Description' => str, 'FTId' => str},...]
#
! # == FT Line; feature table data (>=0, optional)
#
! # Col Data item
! # ----- -----------------
! # 1- 2 FT
! # 6-13 Feature name
! # 15-20 `FROM' endpoint
! # 22-27 `TO' endpoint
! # 35-75 Description (>=0 per key)
! # ----- -----------------
def ft(feature_name = nil)
unless @data['FT']
***************
*** 693,699 ****
# * Keys: ['MW', 'mw', 'molecular', 'weight', 'aalen', 'len', 'length', 'CRC64']
#
! # SQ Line; sequence header (1/entry)
! # SQ SEQUENCE 233 AA; 25630 MW; 146A1B48A1475C86 CRC64;
! # SQ SEQUENCE \d+ AA; \d+ MW; [0-9A-Z]+ CRC64;
#
# MW, Dalton unit.
--- 713,719 ----
# * Keys: ['MW', 'mw', 'molecular', 'weight', 'aalen', 'len', 'length', 'CRC64']
#
! # === SQ Line; sequence header (1/entry)
! # SQ SEQUENCE 233 AA; 25630 MW; 146A1B48A1475C86 CRC64;
! # SQ SEQUENCE \d+ AA; \d+ MW; [0-9A-Z]+ CRC64;
#
# MW, Dalton unit.
Index: uniprot.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/uniprot.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** uniprot.rb 10 Sep 2005 23:43:35 -0000 1.1
--- uniprot.rb 28 Jan 2006 06:40:39 -0000 1.2
***************
*** 1,6 ****
#
! # bio/db/embl/uniprot.rb - UniProt database class
#
! # Copyright (C) 2005 KATAYAMA Toshiaki <k at bioruby.org>
#
# This library is free software; you can redistribute it and/or
--- 1,33 ----
#
! # = bio/db/embl/uniprot.rb - UniProt database class
#
! # Copyright:: Copyright (C) 2005 KATAYAMA Toshiaki <k at bioruby.org>
! # License:: LGPL
! #
! # $Id$
! #
! # == Description
! #
! # Name space for UniProtKB/SwissProt specific methods.
! #
! # UniProtKB/SwissProt specific methods are defined in this class.
! # Shared methods for UniProtKB/SwissProt and TrEMBL classes are
! # defined in Bio::SPTR class.
! #
! # == Examples
! #
! # str = File.read("p53_human.swiss")
! # obj = Bio::UniProt.new(str)
! # obj.entry_id #=> "P53_HUMAN"
! #
! # == Referencees
! #
! # * UniProt
! # http://uniprot.org/
! #
! # * The UniProtKB/SwissProt/TrEMBL User Manual
! # http://www.expasy.org/sprot/userman.html
!
! #--
#
# 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
#
! # $Id$
#
--- 45,49 ----
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! #++
#
***************
*** 25,28 ****
--- 52,57 ----
module Bio
+ # Parser class for SwissProt database entry.
+ # See also Bio::SPTR class.
class UniProt < SPTR
# Nothing to do (UniProt format is abstracted in SPTR)
Index: swissprot.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/swissprot.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** swissprot.rb 23 Aug 2004 23:40:35 -0000 1.3
--- swissprot.rb 28 Jan 2006 06:40:38 -0000 1.4
***************
*** 1,6 ****
#
! # bio/db/embl/swissprot.rb - SwissProt database class
#
! # Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k at bioruby.org>
#
# This library is free software; you can redistribute it and/or
--- 1,33 ----
#
! # = bio/db/embl/swissprot.rb - SwissProt database class
#
! # Copyright:: Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k at bioruby.org>
! # License:: LGPL
! #
! # $Id$
! #
! # == Description
! #
! # Name space for SwissProt specific methods.
! #
! # SwissProt (before UniProtKB/SwissProt) specific methods are defined in
! # this class. Shared methods for UniProtKB/SwissProt and TrEMBL classes
! # are defined in Bio::SPTR class.
! #
! # == Examples
! #
! # str = File.read("p53_human.swiss")
! # obj = Bio::SwissProt.new(str)
! # obj.entry_id #=> "P53_HUMAN"
! #
! # == Referencees
! #
! # * Swiss-Prot Protein knowledgebase
! # http://au.expasy.org/sprot/
! #
! # * Swiss-Prot Protein Knowledgebase User Manual
! # http://au.expasy.org/sprot/userman.html
! #
! #--
#
# 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
#
! # $Id$
#
--- 45,49 ----
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! #++
#
***************
*** 25,28 ****
--- 52,57 ----
module Bio
+ # Parser class for SwissProt database entry.
+ # See also Bio::SPTR class.
class SwissProt < SPTR
# Nothing to do (SwissProt format is abstracted in SPTR)
Index: embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** embl.rb 2 Nov 2005 07:30:14 -0000 1.25
--- embl.rb 28 Jan 2006 06:40:38 -0000 1.26
***************
*** 8,23 ****
# $Id$
#
! # == EMBL database entry
! #
#
#
! # == Example
#
! # emb = Bio::EMBL.new($<.read)
! # emb.entry_id
! # emb.each_cds do |cds|
! # cds
! # end
! # emb.seq
#
#--
--- 8,31 ----
# $Id$
#
! # == Description
#
+ # Parser class for EMBL database entry.
#
! # == Examples
#
! # emb = Bio::EMBL.new($<.read)
! # emb.entry_id
! # emb.each_cds do |cds|
! # cds # A CDS in feature table.
! # end
! # emb.seq #=> "ACGT..."
! #
! # == References
! #
! # * The EMBL Nucleotide Sequence Database
! # http://www.ebi.ac.uk/embl/
! #
! # * The EMBL Nucleotide Sequence Database: Users Manual
! # http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
#
#--
Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** common.rb 2 Nov 2005 07:30:14 -0000 1.8
--- common.rb 28 Jan 2006 06:40:38 -0000 1.9
***************
*** 7,14 ****
# $Id$
#
! # == EMBL style databases class
#
! # This module defines a common framework among EMBL, SWISS-PROT, TrEMBL.
! # For more details, see the documentations in each embl/*.rb libraries.
#
# EMBL style format:
--- 7,17 ----
# $Id$
#
! # == Description
#
! # EMBL style databases class
! #
! # This module defines a common framework among EMBL, UniProtKB, SWISS-PROT,
! # TrEMBL. For more details, see the documentations in each embl/*.rb
! # libraries.
#
# EMBL style format:
***************
*** 39,45 ****
# // - termination line (ends each entry; 1 per entry)
#
! #
! # == Example
#
# require 'bio/db/embl/common'
# module Bio
--- 42,48 ----
# // - termination line (ends each entry; 1 per entry)
#
! # == Examples
#
+ # # Make a new parser class for EMBL style database entry.
# require 'bio/db/embl/common'
# module Bio
***************
*** 48,51 ****
--- 51,72 ----
# end
# end
+ #
+ # == References
+ #
+ # * The EMBL Nucleotide Sequence Database
+ # http://www.ebi.ac.uk/embl/
+ #
+ # * The EMBL Nucleotide Sequence Database: Users Manual
+ # http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
+ #
+ # * Swiss-Prot Protein knowledgebase. TrEMBL Computer-annotated supplement
+ # to Swiss-Prot
+ # http://au.expasy.org/sprot/
+ #
+ # * UniProt
+ # http://uniprot.org/
+ #
+ # * The UniProtKB/SwissProt/TrEMBL User Manual
+ # http://www.expasy.org/sprot/userman.html
#
#--
Index: trembl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/trembl.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** trembl.rb 23 Aug 2004 23:40:35 -0000 1.3
--- trembl.rb 28 Jan 2006 06:40:38 -0000 1.4
***************
*** 1,6 ****
#
! # bio/db/embl/trembl.rb - TrEMBL database class
#
! # Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k at bioruby.org>
#
# This library is free software; you can redistribute it and/or
--- 1,33 ----
#
! # = bio/db/embl/trembl.rb - TrEMBL database class
#
! # Copyright:: Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k at bioruby.org>
! # License:: LGPL
! #
! # $Id$
! #
! # == Description
! #
! # Name space for TrEMBL specific methods.
! #
! # UniProtKB/SwissProt specific methods are defined in this class.
! # Shared methods for UniProtKB/SwissProt and TrEMBL classes are
! # defined in Bio::SPTR class.
! #
! # == Examples
! #
! # str = File.read("Q2UNG2_ASPOR.trembl")
! # obj = Bio::TrEMBL.new(str)
! # obj.entry_id #=> "Q2UNG2_ASPOR"
! #
! # == Referencees
! #
! # * TrEMBL Computer-annotated supplement to Swiss-Prot
! # http://au.expasy.org/sprot/
! #
! # * TrEMBL Computer-annotated supplement to Swiss-Prot User Manual
! # http://au.expasy.org/sprot/userman.html
! #
! #--
#
# 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
#
! # $Id$
#
--- 45,49 ----
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! #++
#
***************
*** 25,28 ****
--- 52,57 ----
module Bio
+ # Parser class for TrEMBL database entry.
+ # See also Bio::SPTR class.
class TrEMBL < SPTR
# Nothing to do (TrEMBL format is abstracted in SPTR)
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