[BioRuby-cvs] bioruby/lib/bio/db/embl sptr.rb,1.25,1.26
Mitsuteru C. Nakao
nakao at pub.open-bio.org
Sun Oct 23 04:59:45 EDT 2005
Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory pub.open-bio.org:/tmp/cvs-serv18595/lib/bio/db/embl
Modified Files:
sptr.rb
Log Message:
* Changed to rdoc format.
* Bio::EMBL::Common changed to Bio::EMBLDB::Common.
Index: sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** sptr.rb 26 Sep 2005 13:00:06 -0000 1.25
--- sptr.rb 23 Oct 2005 08:59:43 -0000 1.26
***************
*** 1,6 ****
#
! # bio/db/embl/sptr.rb - SwissProt and TrEMBL database class
#
! # Copyright (C) 2001-2003 Mitsuteru C. Nakao <n at bioruby.org>
#
# This library is free software; you can redistribute it and/or
--- 1,18 ----
#
! # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
#
! # Author:: Mitsuteru C. Nakao <n at bioruby.org>
! # Copyright:: Copyright (C) 2001-2005 BioRuby Project
! # License:: LGPL
! #
! # $Id$
! #
! # == UniProtKB/SwissProt and TrEMBL
! #
! # See the SWISS-PROT dicument file SPECLIST.TXT.
! #
! # == Example
! #
! #--
#
# This library is free software; you can redistribute it and/or
***************
*** 18,52 ****
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! # $Id$
#
require 'bio/db'
module Bio
class SPTR < EMBLDB
!
! require 'bio/db/embl/common'
! include Bio::EMBL::Common
! # ID Line
#
# "ID #{ENTRY_NAME} #{DATA_CLASS}; #{MOLECULE_TYPE}; #{SEQUENCE_LENGTH}."
#
! # ENTRY_NAME = "#{X}_#{Y}"
! # X =~ /[A-Z0-9]{1,4}/ # The protein name.
# Y =~ /[A-Z0-9]{1,5}/ # The biological source of the protein.
! # MOLECULE_TYPE = 'PRT' =~ /\w{3}/
# SEQUENCE_LENGTH =~ /\d+ AA/
- #
- # See also the SWISS-PROT dicument file SPECLIST.TXT.
- #
-
- @@entry_regrexp = /[A-Z0-9]{1,4}_[A-Z0-9]{1,5}/
- @@data_class = ["STANDARD", "PRELIMINARY"]
-
- # Bio::SPTR#id_line -> hsh
- # Bio::SPTR#id_line(key) -> str or int
def id_line(key = nil)
unless @data['ID']
--- 30,61 ----
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! #++
#
require 'bio/db'
+ require 'bio/db/embl/common'
module Bio
+ # Parser class for UniProtKB/SwissProt and TrEMBL database entry
class SPTR < EMBLDB
! include Bio::EMBLDB::Common
+ @@entry_regrexp = /[A-Z0-9]{1,4}_[A-Z0-9]{1,5}/
+ @@data_class = ["STANDARD", "PRELIMINARY"]
!
! # 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']
***************
*** 67,78 ****
end
#
! def entry
id_line('ENTRY_NAME')
end
! alias entry_name entry
! alias entry_id entry
#
def molecule
id_line('MOLECULE_TYPE')
--- 76,94 ----
end
+
+
+ # 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')
end
! alias entry_name entry_id
! alias entry entry_id
+
+ # returns a MOLECULE_TYPE in the ID line.
#
+ # A short-cut for Bio::SPTR#id_line('MOLECULE_TYPE').
def molecule
id_line('MOLECULE_TYPE')
***************
*** 80,84 ****
alias molecule_type molecule
! #
def sequence_length
id_line('SEQUENCE_LENGTH')
--- 96,103 ----
alias molecule_type molecule
!
! # returns a SEQUENCE_LENGTH in the ID line.
! #
! # A short-cut for Bio::SPTR#id_line('SEQUENCE_LENGHT').
def sequence_length
id_line('SEQUENCE_LENGTH')
***************
*** 87,115 ****
! # AC Line
! #
! # "AC A12345; B23456;"
! #
! # AC [AC1;]+
! #
! # Accession numbers format:
! # 1 2 3 4 5 6
! # [O,P,Q] [0-9] [A-Z, 0-9] [A-Z, 0-9] [A-Z, 0-9] [0-9]
! #
! # Bio::SPTR#ac -> ary
! # #accessions -> ary
! # #accession -> accessions.first
!
@@ac_regrexp = /[OPQ][0-9][A-Z0-9]{3}[0-9]/
! # 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)
#
! # Bio::SPTR#dt -> Hash
! # Bio::SPTR#dt(key) -> String
! # key = (created|sequence|annotation)
def dt(key = nil)
unless @data['DT']
--- 106,128 ----
! # Bio::EMBL::Common#ac -> ary
! # #accessions -> ary
! # #accession -> String (accessions.first)
@@ac_regrexp = /[OPQ][0-9][A-Z0-9]{3}[0-9]/
!
! # returns a Hash of information in the DT lines.
! # hash keys:
! # ['created', 'sequence', 'annotation']
! # also Symbols acceptable (ASAP):
! # [:created, :sequence, :annotation]
#
! # 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']
***************
*** 130,141 ****
# DE Line; description (>=1)
! # "DE #{OFFICIAL_NAME} (#{SYNONYM})"
! # "DE #{OFFICIAL_NAME} (#{SYNONYM}) [CONTEINS: #1; #2]."
! # OFFICIAL_NAME 1/entry
! # SYNONYM >=0
! # CONTEINS >=0
! #
! # Returns the proposed official name of the protein
def protein_name
name = ""
--- 143,154 ----
+ # returns the proposed official name of the protein.
+ #
# DE Line; description (>=1)
! # "DE #{OFFICIAL_NAME} (#{SYNONYM})"
! # "DE #{OFFICIAL_NAME} (#{SYNONYM}) [CONTEINS: #1; #2]."
! # OFFICIAL_NAME 1/entry
! # SYNONYM >=0
! # CONTEINS >=0
def protein_name
name = ""
***************
*** 147,152 ****
return name
end
! # synonyms are each placed in () following the official name on the DE line
! # Returns an array of synonyms (unofficial names)
def synonyms
ary = Array.new
--- 160,168 ----
return name
end
!
!
! # returns an array of synonyms (unofficial names).
! #
! # synonyms are each placed in () following the official name on the DE line.
def synonyms
ary = Array.new
***************
*** 163,166 ****
--- 179,197 ----
+ # returns gene names in the GN line.
+ #
+ # New UniProt/SwissProt format:
+ # * Bio::SPTR#gn -> [ <gene record>* ]
+ # where <gene record> is:
+ # { :name => '...',
+ # :synonyms => [ 's1', 's2', ... ],
+ # :loci => [ 'l1', 'l2', ... ],
+ # :orfs => [ 'o1', 'o2', ... ]
+ # }
+ #
+ # Old format:
+ # * Bio::SPTR#gn -> Array # AND
+ # * Bio::SPTR#gn[0] -> Array # OR
+ #
# GN Line: Gene name(s) (>=0, optional)
def gn
***************
*** 176,189 ****
# GN Line: Gene name(s) (>=0, optional)
! # GN HNS OR DRDX OR OSMZ OR BGLY.
! # GN CECA1 AND CECA2.
! # GN CECA1 AND (HOGE OR FUGA).
#
! # GN NAME1 [(AND|OR) NAME]+.
#
# Bio::SPTR#gn -> Array # AND
# #gn[0] -> Array # OR
# #gene_names -> Array
- #
def gn_old_parser
names = Array.new
--- 207,219 ----
# GN Line: Gene name(s) (>=0, optional)
! # GN HNS OR DRDX OR OSMZ OR BGLY.
! # GN CECA1 AND CECA2.
! # GN CECA1 AND (HOGE OR FUGA).
#
! # GN NAME1 [(AND|OR) NAME]+.
#
# Bio::SPTR#gn -> Array # AND
# #gn[0] -> Array # OR
# #gene_names -> Array
def gn_old_parser
names = Array.new
***************
*** 202,212 ****
# The new format of the GN line is:
! # GN Name=; Synonyms=[, ...]; OrderedLocusNames=[, ...];
! # GN ORFNames=[, ...];
! #
! # GN and
#
! # Bio::SPTR#gn -> [ <gene record>* ]
! # where <gene record> is:
# { :name => '...',
# :synonyms => [ 's1', 's2', ... ],
--- 232,240 ----
# The new format of the GN line is:
! # GN Name=; Synonyms=[, ...]; OrderedLocusNames=[, ...];
! # GN ORFNames=[, ...];
#
! # * Bio::SPTR#gn -> [ <gene record>* ]
! # where <gene record> is:
# { :name => '...',
# :synonyms => [ 's1', 's2', ... ],
***************
*** 239,243 ****
! # Bio::SPTR#gene_names -> [String]
def gene_names
gn # set @data['GN'] if it hasn't been already done
--- 267,271 ----
! # returns a Array of gene names in the GN line.
def gene_names
gn # set @data['GN'] if it hasn't been already done
***************
*** 250,255 ****
! # Bio::SPTR#gene_name -> String
! #
def gene_name
gene_names.first
--- 278,282 ----
! # returns a String of the first gene name in the GN line.
def gene_name
gene_names.first
***************
*** 257,276 ****
# OS Line; organism species (>=1)
! # "OS Genus species (name)."
! # "OS Genus species (name0) (name1)."
! # "OS Genus species (name0) (name1)."
! # "OS Genus species (name0), G s0 (name0), and G s (name0) (name1)."
! # "OS Homo sapiens (Human), and Rarrus norveticus (Rat)"
! #
! # Bio::EMBLDB#os -> Array of Hash
! # [{'name'=>'(Human)', 'os'=>'Homo sapiens'},
! # {'name'=>'(Rat)', 'os'=>'Rattus norveticus'}]
! # Bio::SPTR#os[0]['name'] => "(Human)"
! # Bio::EPTR#os[0] => {'name'=>"(Human)", 'os'=>'Homo sapiens'}
! # Bio::EPTR#os(0) => "Homo sapiens (Human)"
! #
! # Bio::SPTR#os -> Array of Hash
! # Bio::SPTR#os(num) -> String
def os(num = nil)
unless @data['OS']
--- 284,302 ----
+ # returns a Array of Hashs or a String of the OS line when a key given.
+ # * Bio::EMBLDB#os -> Array
+ # [{'name' => '(Human)', 'os' => 'Homo sapiens'},
+ # {'name' => '(Rat)', 'os' => 'Rattus norveticus'}]
+ # * Bio::EPTR#os[0] -> Hash
+ # {'name' => "(Human)", 'os' => 'Homo sapiens'}
+ # * Bio::SPTR#os[0]['name'] -> "(Human)"
+ # * Bio::EPTR#os(0) -> "Homo sapiens (Human)"
+ #
# OS Line; organism species (>=1)
! # OS Genus species (name).
! # OS Genus species (name0) (name1).
! # OS Genus species (name0) (name1).
! # OS Genus species (name0), G s0 (name0), and G s (name0) (name1).
! # OS Homo sapiens (Human), and Rarrus norveticus (Rat)
def os(num = nil)
unless @data['OS']
***************
*** 297,318 ****
# OG Line; organella (0 or 1/entry)
# ["MITOCHONDRION", "CHLOROPLAST", "Cyanelle", "Plasmid"]
# or a plasmid name (e.g. "Plasmid pBR322").
- #
- # Bio::SPTR#og -> Array
# OC Line; organism classification (>=1)
! # OC Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae;
! # OC Theileria.
! #
! # Bio::EMBLDB#oc -> Array
! # OX Line; organism taxonomy cross-reference (>=1 per entry)
! # OX NCBI_TaxID=1234;
! # OX NCBI_TaxID=1234, 2345, 3456, 4567;
#
! # Bio::SPTR#ox -> {'NCBI_TaxID' => ['1234','2345','3456','4567']}
def ox
unless @data['OX']
--- 323,346 ----
+ # Bio::EMBL::Common#og -> Array
# OG Line; organella (0 or 1/entry)
# ["MITOCHONDRION", "CHLOROPLAST", "Cyanelle", "Plasmid"]
# or a plasmid name (e.g. "Plasmid pBR322").
+ # Bio::EMBL::Common#oc -> Array
# OC Line; organism classification (>=1)
! # "OC Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae;"
! # "OC Theileria."
!
!
! # 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;
def ox
unless @data['OX']
***************
*** 328,345 ****
end
!
# R Lines
# RN RC RP RX RA RT RL
- # Bio::EMBLDB#ref -> Array
- # 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.
- #
- # CC -!- CAUTION: HOGE HOGE IS FUGA FUGA!
- #
@@cc_topics = ['ALTERNATIVE PRODUCTS','CATALYTIC ACTIVITY','CAUTION',
--- 356,364 ----
end
!
! # Bio::EMBL::Common#ref -> Array
# R Lines
# RN RC RP RX RA RT RL
@@cc_topics = ['ALTERNATIVE PRODUCTS','CATALYTIC ACTIVITY','CAUTION',
***************
*** 348,373 ****
'MISCELLANEOUS','PATHWAY','PHARMACEUTICAL','POLYMORPHISM','PTM',
'SIMILARITY','SUBCELLULAR LOCATION','SUBUNIT','TISSUE SPECIFICITY']
! # DATABASE: NAME=Text[; NOTE=Text][; WWW="Address"][; FTP="Address"].
! # MASS SPECTROMETRY: MW=XXX[; MW_ERR=XX][; METHOD=XX][;RANGE=XX-XX].
#
! # Bio::SPTR#cc -> Hash w/in Array
! # Bio::SPTR#cc(Int) -> String
! # Bio::SPTR#cc(TOPIC) -> Array w/in Hash
! # Bio::SPTR#cc('ALTERNATIVE PRODUCTS') -> {'Event'=>str,
! # 'Named isoforms'=>int,
! # 'Comment'=>str,
! # 'Variants'=>[{'Name'=>str,
! # 'Synonyms'=>str,
! # 'IsoId'=>str,
! # 'Sequence'=>[]}]}
! # Bio::SPTR#cc('DATABASE') -> [{'NAME'=>str,'NOTE'=>str,
! # 'WWW'=>URI,'FTP'=>URI}]
! # Bio::SPTR#cc('MASS SPECTROMETRY') -> [{'MW"=>float,'MW_ERR'=>float,
! # 'METHOD'=>str,'RANGE'=>str}]
#
def cc(tag = nil)
-
- # @data['CC'] = {'DATABASE'=>['hoge','fuga'], ... }
unless @data['CC']
cc = Hash.new
--- 367,410 ----
'MISCELLANEOUS','PATHWAY','PHARMACEUTICAL','POLYMORPHISM','PTM',
'SIMILARITY','SUBCELLULAR LOCATION','SUBUNIT','TISSUE SPECIFICITY']
+ # 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']
cc = Hash.new
***************
*** 405,409 ****
end
-
case tag
when 'ALTERNATIVE PRODUCTS'
--- 442,445 ----
***************
*** 411,421 ****
return ap unless ap
- # 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;
-
# Event, Named isoforms, Comment, [Name, Synonyms, IsoId, Sequnce]+
tmp = {'Event' => nil, 'Named isoforms' => nil, 'Comment' => nil, 'Variants' => []}
--- 447,450 ----
***************
*** 508,516 ****
# DR Line; defabases cross-reference (>=0)
# a cross_ref pre one line
! # "DR database_identifier; primary_identifier; secondary_identifier."
! # Bio::EMBLDB#dr -> Hash w/in Array
!
@@dr_database_identifier = ['EMBL','CARBBANK','DICTYDB','ECO2DBASE',
'ECOGENE',
--- 537,546 ----
+ # returns databases cross-references in the DR lines.
+ # * 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',
***************
*** 520,544 ****
'SWISS-2DPAGE','TIGR','TRANSFAC','TUBERCULIST','WORMPEP','YEPD','ZFIN']
!
# KW Line; keyword (>=1)
# KW [Keyword;]+
- # Bio::EMBLDB#kw -> Array
- # #keywords -> Array
! # 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)
! # ----- -----------------
#
! # Bio::SPTR#ft -> {'feature_name'=>[{'From'=>str,'To'=>str,
! # 'Description'=>str, 'FTId'=>str}],}
! # Bio::SPTR#ft(feature_name) -> [{'From'=>str,'To'=>str,
! # 'Description'=>str, 'FTId'=>str},...]
def ft(feature_name = nil)
unless @data['FT']
--- 550,579 ----
'SWISS-2DPAGE','TIGR','TRANSFAC','TUBERCULIST','WORMPEP','YEPD','ZFIN']
! # Bio::EMBL::Common#kw - Array
! # #keywords -> Array
! #
# KW Line; keyword (>=1)
# KW [Keyword;]+
!
! # 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']
***************
*** 635,648 ****
! # 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
! # CRC64 (64-bit Cyclic Redundancy Check, ISO 3309)
#
! # Bio::SPTRL#sq -> hsh
! # Bio::SPTRL#sq(key) -> int or str
#
def sq(key = nil)
unless @data['SQ']
--- 670,686 ----
! # returns a Hash of conteins in the SQ lines.
! # * Bio::SPTRL#sq -> hsh
#
! # returns a value of a key given in the SQ lines.
! # * Bio::SPTRL#sq(key) -> int or str
! # * 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.
+ # CRC64 (64-bit Cyclic Redundancy Check, ISO 3309).
def sq(key = nil)
unless @data['SQ']
***************
*** 668,675 ****
end
! # @orig[''] as sequence
! # blank Line; sequence data (>=1)
! # Bio::SPTR#seq -> Bio::Sequence::AA
#
def seq
unless @data['']
--- 706,714 ----
end
!
! # returns a Bio::Sequence::AA of the amino acid sequence.
! # * Bio::SPTR#seq -> Bio::Sequence::AA
#
+ # blank Line; sequence data (>=1)
def seq
unless @data['']
***************
*** 680,686 ****
alias aaseq seq
! end
! end
--- 719,725 ----
alias aaseq seq
! end # class SPTR
! end # module Bio
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