[BioRuby-cvs] bioruby/lib/bio/db prosite.rb, 0.15, 0.16 nbrf.rb, 1.8, 1.9 medline.rb, 1.14, 1.15 litdb.rb, 0.8, 0.9 fasta.rb, 1.25, 1.26
Katayama Toshiaki
k at dev.open-bio.org
Tue Sep 19 06:03:53 UTC 2006
Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory dev.open-bio.org:/tmp/cvs-serv32475/lib/bio/db
Modified Files:
prosite.rb nbrf.rb medline.rb litdb.rb fasta.rb
Log Message:
* minor doc fix
Index: prosite.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/prosite.rb,v
retrieving revision 0.15
retrieving revision 0.16
diff -C2 -d -r0.15 -r0.16
*** prosite.rb 25 Jul 2006 18:53:56 -0000 0.15
--- prosite.rb 19 Sep 2006 06:03:51 -0000 0.16
***************
*** 2,9 ****
# = bio/db/prosite.rb - PROSITE database class
#
! # Copyright:: Copyright (C) 2001 KATAYAMA Toshiaki <k at bioruby.org>
# Licence:: Ruby's
#
! # $Id$
#
--- 2,9 ----
# = bio/db/prosite.rb - PROSITE database class
[...978 lines suppressed...]
+ def re
+ self.class.pa2re(self.pa)
+ end
+ ### prosite profile to regular expression
+ #
+ # prosite/profile.txt:
+ #
+ # Returns
+ def ma2re(matrix)
+ raise NotImplementedError
end
! end # PROSITE
!
! end # Bio
Index: litdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/litdb.rb,v
retrieving revision 0.8
retrieving revision 0.9
diff -C2 -d -r0.8 -r0.9
*** litdb.rb 8 May 2006 14:22:12 -0000 0.8
--- litdb.rb 19 Sep 2006 06:03:51 -0000 0.9
***************
*** 2,9 ****
# = bio/db/litdb.rb - LITDB database class
#
! # Copyright:: Copyright (C) 2001 KATAYAMA Toshiaki <k at bioruby.org>
# License:: Ruby's
#
! # $Id$
#
--- 2,9 ----
# = bio/db/litdb.rb - LITDB database class
#
! # Copyright:: Copyright (C) 2001 Toshiaki Katayama <k at bioruby.org>
# License:: Ruby's
#
! # $Id$
#
Index: fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/fasta.rb,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** fasta.rb 22 Feb 2006 08:44:46 -0000 1.25
--- fasta.rb 19 Sep 2006 06:03:51 -0000 1.26
***************
*** 4,8 ****
# Copyright:: Copyright (C) 2001, 2002
# GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>,
! # KATAYAMA Toshiaki <k at bioruby.org>
# Lisence:: Ruby's
#
--- 4,8 ----
# Copyright:: Copyright (C) 2001, 2002
# GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>,
! # Toshiaki Katayama <k at bioruby.org>
# Lisence:: Ruby's
#
Index: medline.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/medline.rb,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** medline.rb 8 May 2006 14:22:41 -0000 1.14
--- medline.rb 19 Sep 2006 06:03:51 -0000 1.15
***************
*** 3,9 ****
#
# Copyright:: Copyright (C) 2001, 2005
! # KATAYAMA Toshiaki <k at bioruby.org>
# License:: Ruby's
#
# == Description
#
--- 3,16 ----
#
# Copyright:: Copyright (C) 2001, 2005
! # Toshiaki Katayama <k at bioruby.org>
# License:: Ruby's
#
+ # $Id$
+ #
+
+ require 'bio/db'
+
+ module Bio
+
# == Description
#
***************
*** 17,317 ****
# medilne.mesh
#
! # $Id$
! #
!
! require 'bio/db'
!
! module Bio
!
! # NCBI PubMed/MEDLINE database class.
! class MEDLINE < NCBIDB
! #
! def initialize(entry)
! @pubmed = Hash.new('')
! tag = ''
! entry.each_line do |line|
! if line =~ /^\w/
! tag = line[0,4].strip
! end
! @pubmed[tag] += line[6..-1] if line.length > 6
end
end
! # returns a Reference object.
! def reference
! hash = Hash.new('')
! hash['authors'] = authors
! hash['title'] = title
! hash['journal'] = journal
! hash['volume'] = volume
! hash['issue'] = issue
! hash['pages'] = pages
! hash['year'] = year
! hash['pubmed'] = pmid
! hash['medline'] = ui
! hash['abstract'] = abstract
! hash['mesh'] = mesh
! hash['affiliations'] = affiliations
! hash.delete_if { |k, v| v.nil? or v.empty? }
! return Reference.new(hash)
! end
! ### Common MEDLINE tags
! # PMID - PubMed Unique Identifier
! # Unique number assigned to each PubMed citation.
! def pmid
! @pubmed['PMID'].strip
! end
! alias entry_id pmid
! # UI - MEDLINE Unique Identifier
! # Unique number assigned to each MEDLINE citation.
! def ui
! @pubmed['UI'].strip
! end
! # TA - Journal Title Abbreviation
! # Standard journal title abbreviation.
! def ta
! @pubmed['TA'].gsub(/\s+/, ' ').strip
! end
! alias journal ta
! # VI - Volume
! # Journal volume.
! def vi
! @pubmed['VI'].strip
! end
! alias volume vi
! # IP - Issue
! # The number of the issue, part, or supplement of the journal in which
! # the article was published.
! def ip
! @pubmed['IP'].strip
! end
! alias issue ip
! # PG - Page Number
! # The full pagination of the article.
! def pg
! @pubmed['PG'].strip
! end
! def pages
! pages = pg
! if pages =~ /-/
! from, to = pages.split('-')
! if (len = from.length - to.length) > 0
! to = from[0,len] + to
! end
! pages = "#{from}-#{to}"
end
! return pages
end
! # DP - Publication Date
! # The date the article was published.
! def dp
! @pubmed['DP'].strip
! end
! alias date dp
! def year
! dp[0,4]
! end
! # TI - Title Words
! # The title of the article.
! def ti
! @pubmed['TI'].gsub(/\s+/, ' ').strip
! end
! alias title ti
! # AB - Abstract
! # Abstract.
! def ab
! @pubmed['AB'].gsub(/\s+/, ' ').strip
! end
! alias abstract ab
! # AU - Author Name
! # Authors' names.
! def au
! @pubmed['AU'].strip
! end
! def authors
! authors = []
! au.split(/\n/).each do |author|
! if author =~ / /
! name = author.split(/\s+/)
! suffix = name[-2] =~ /^[A-Z]+$/ ? name.pop : nil # Jr etc.
! initial = name.pop.split(//).join('. ')
! author = "#{name.join(' ')}, #{initial}."
! end
! if suffix
! author << " " + suffix
! end
! authors.push(author)
end
! return authors
end
! # SO - Source
! # Composite field containing bibliographic information.
! def so
! @pubmed['SO'].strip
! end
! alias source so
! # MH - MeSH Terms
! # NLM's controlled vocabulary.
! def mh
! @pubmed['MH'].strip.split(/\n/)
! end
! alias mesh mh
! # AD - Affiliation
! # Institutional affiliation and address of the first author, and grant
! # numbers.
! def ad
! @pubmed['AD'].strip.split(/\n/)
! end
! alias affiliations ad
! ### Other MEDLINE tags
! # AID - Article Identifier
! # Article ID values may include the pii (controlled publisher identifier)
! # or doi (Digital Object Identifier).
! # CI - Copyright Information
! # Copyright statement.
! # CIN - Comment In
! # Reference containing a comment about the article.
! # CN - Collective Name
! # Corporate author or group names with authorship responsibility.
! # CON - Comment On
! # Reference upon which the article comments.
! # CY - Country
! # The place of publication of the journal.
! # DA - Date Created
! # Used for internal processing at NLM.
! # DCOM - Date Completed
! # Used for internal processing at NLM.
! # DEP - Date of Electronic Publication
! # Electronic publication date.
! # EDAT - Entrez Date
! # The date the citation was added to PubMed.
! # EIN - Erratum In
! # Reference containing a published erratum to the article.
! # GS - Gene Symbol
! # Abbreviated gene names (used 1991 through 1996).
! # ID - Identification Number
! # Research grant numbers, contract numbers, or both that designate
! # financial support by any agency of the US PHS (Public Health Service).
! # IS - ISSN
! # International Standard Serial Number of the journal.
! # JC - Journal Title Code
! # MEDLINE unique three-character code for the journal.
! # JID - NLM Unique ID
! # Unique journal ID in NLM's catalog of books, journals, and audiovisuals.
! # LA - Language
! # The language in which the article was published.
! # LR - Last Revision Date
! # The date a change was made to the record during a maintenance procedure.
! # MHDA - MeSH Date
! # The date MeSH terms were added to the citation. The MeSH date is the
! # same as the Entrez date until MeSH are added.
! # PHST - Publication History Status Date
! # History status date.
! # PS - Personal Name as Subject
! # Individual is the subject of the article.
! # PST - Publication Status
! # Publication status.
! # PT - Publication Type
! # The type of material the article represents.
! def pt
! @pubmed['PT'].strip.split(/\n/)
! end
! alias publication_type pt
! # RF - Number of References
! # Number of bibliographic references for Review articles.
! # RIN - Retraction In
! # Retraction of the article
! # RN - EC/RN Number
! # Number assigned by the Enzyme Commission to designate a particular
! # enzyme or by the Chemical Abstracts Service for Registry Numbers.
! # ROF - Retraction Of
! # Article being retracted.
! # RPF - Republished From
! # Original article.
! # SB - Journal Subset
! # Code for a specific set of journals.
! # SI - Secondary Source Identifier
! # Identifies a secondary source that supplies information, e.g., other
! # data sources, databanks and accession numbers of molecular sequences
! # discussed in articles.
! # TT - Transliterated / Vernacular Title
! # Non-Roman alphabet language titles are transliterated.
! # UIN - Update In
! # Update to the article.
! # UOF - Update Of
! # The article being updated.
! # URLF - URL Full-Text
! # Link to the full-text of article at provider's website. Links are
! # incomplete. Use PmLink for the complete set of available links.
! # [PmLink] http://www.ncbi.nlm.nih.gov/entrez/utils/pmlink_help.html
! # URLS - URL Summary
! # Link to the article summary at provider's website. Links are
! # incomplete. Use PmLink for the complete set of available links.
! # [PmLink] http://www.ncbi.nlm.nih.gov/entrez/utils/pmlink_help.html
! end
! end
--- 24,316 ----
# medilne.mesh
#
! class MEDLINE < NCBIDB
! #
! def initialize(entry)
! @pubmed = Hash.new('')
! tag = ''
! entry.each_line do |line|
! if line =~ /^\w/
! tag = line[0,4].strip
end
+ @pubmed[tag] += line[6..-1] if line.length > 6
end
+ end
! # returns a Reference object.
! def reference
! hash = Hash.new('')
! hash['authors'] = authors
! hash['title'] = title
! hash['journal'] = journal
! hash['volume'] = volume
! hash['issue'] = issue
! hash['pages'] = pages
! hash['year'] = year
! hash['pubmed'] = pmid
! hash['medline'] = ui
! hash['abstract'] = abstract
! hash['mesh'] = mesh
! hash['affiliations'] = affiliations
! hash.delete_if { |k, v| v.nil? or v.empty? }
! return Reference.new(hash)
! end
! ### Common MEDLINE tags
! # PMID - PubMed Unique Identifier
! # Unique number assigned to each PubMed citation.
! def pmid
! @pubmed['PMID'].strip
! end
! alias entry_id pmid
! # UI - MEDLINE Unique Identifier
! # Unique number assigned to each MEDLINE citation.
! def ui
! @pubmed['UI'].strip
! end
! # TA - Journal Title Abbreviation
! # Standard journal title abbreviation.
! def ta
! @pubmed['TA'].gsub(/\s+/, ' ').strip
! end
! alias journal ta
! # VI - Volume
! # Journal volume.
! def vi
! @pubmed['VI'].strip
! end
! alias volume vi
! # IP - Issue
! # The number of the issue, part, or supplement of the journal in which
! # the article was published.
! def ip
! @pubmed['IP'].strip
! end
! alias issue ip
! # PG - Page Number
! # The full pagination of the article.
! def pg
! @pubmed['PG'].strip
! end
! def pages
! pages = pg
! if pages =~ /-/
! from, to = pages.split('-')
! if (len = from.length - to.length) > 0
! to = from[0,len] + to
end
! pages = "#{from}-#{to}"
end
+ return pages
+ end
! # DP - Publication Date
! # The date the article was published.
! def dp
! @pubmed['DP'].strip
! end
! alias date dp
! def year
! dp[0,4]
! end
! # TI - Title Words
! # The title of the article.
! def ti
! @pubmed['TI'].gsub(/\s+/, ' ').strip
! end
! alias title ti
! # AB - Abstract
! # Abstract.
! def ab
! @pubmed['AB'].gsub(/\s+/, ' ').strip
! end
! alias abstract ab
! # AU - Author Name
! # Authors' names.
! def au
! @pubmed['AU'].strip
! end
! def authors
! authors = []
! au.split(/\n/).each do |author|
! if author =~ / /
! name = author.split(/\s+/)
! suffix = name[-2] =~ /^[A-Z]+$/ ? name.pop : nil # Jr etc.
! initial = name.pop.split(//).join('. ')
! author = "#{name.join(' ')}, #{initial}."
end
! if suffix
! author << " " + suffix
! end
! authors.push(author)
end
+ return authors
+ end
! # SO - Source
! # Composite field containing bibliographic information.
! def so
! @pubmed['SO'].strip
! end
! alias source so
! # MH - MeSH Terms
! # NLM's controlled vocabulary.
! def mh
! @pubmed['MH'].strip.split(/\n/)
! end
! alias mesh mh
! # AD - Affiliation
! # Institutional affiliation and address of the first author, and grant
! # numbers.
! def ad
! @pubmed['AD'].strip.split(/\n/)
! end
! alias affiliations ad
! ### Other MEDLINE tags
! # AID - Article Identifier
! # Article ID values may include the pii (controlled publisher identifier)
! # or doi (Digital Object Identifier).
! # CI - Copyright Information
! # Copyright statement.
! # CIN - Comment In
! # Reference containing a comment about the article.
! # CN - Collective Name
! # Corporate author or group names with authorship responsibility.
! # CON - Comment On
! # Reference upon which the article comments.
! # CY - Country
! # The place of publication of the journal.
! # DA - Date Created
! # Used for internal processing at NLM.
! # DCOM - Date Completed
! # Used for internal processing at NLM.
! # DEP - Date of Electronic Publication
! # Electronic publication date.
! # EDAT - Entrez Date
! # The date the citation was added to PubMed.
! # EIN - Erratum In
! # Reference containing a published erratum to the article.
! # GS - Gene Symbol
! # Abbreviated gene names (used 1991 through 1996).
! # ID - Identification Number
! # Research grant numbers, contract numbers, or both that designate
! # financial support by any agency of the US PHS (Public Health Service).
! # IS - ISSN
! # International Standard Serial Number of the journal.
! # JC - Journal Title Code
! # MEDLINE unique three-character code for the journal.
! # JID - NLM Unique ID
! # Unique journal ID in NLM's catalog of books, journals, and audiovisuals.
! # LA - Language
! # The language in which the article was published.
! # LR - Last Revision Date
! # The date a change was made to the record during a maintenance procedure.
! # MHDA - MeSH Date
! # The date MeSH terms were added to the citation. The MeSH date is the
! # same as the Entrez date until MeSH are added.
! # PHST - Publication History Status Date
! # History status date.
! # PS - Personal Name as Subject
! # Individual is the subject of the article.
! # PST - Publication Status
! # Publication status.
! # PT - Publication Type
! # The type of material the article represents.
! def pt
! @pubmed['PT'].strip.split(/\n/)
! end
! alias publication_type pt
! # RF - Number of References
! # Number of bibliographic references for Review articles.
! # RIN - Retraction In
! # Retraction of the article
! # RN - EC/RN Number
! # Number assigned by the Enzyme Commission to designate a particular
! # enzyme or by the Chemical Abstracts Service for Registry Numbers.
! # ROF - Retraction Of
! # Article being retracted.
! # RPF - Republished From
! # Original article.
! # SB - Journal Subset
! # Code for a specific set of journals.
! # SI - Secondary Source Identifier
! # Identifies a secondary source that supplies information, e.g., other
! # data sources, databanks and accession numbers of molecular sequences
! # discussed in articles.
! # TT - Transliterated / Vernacular Title
! # Non-Roman alphabet language titles are transliterated.
! # UIN - Update In
! # Update to the article.
! # UOF - Update Of
! # The article being updated.
! # URLF - URL Full-Text
! # Link to the full-text of article at provider's website. Links are
! # incomplete. Use PmLink for the complete set of available links.
! # [PmLink] http://www.ncbi.nlm.nih.gov/entrez/utils/pmlink_help.html
! # URLS - URL Summary
! # Link to the article summary at provider's website. Links are
! # incomplete. Use PmLink for the complete set of available links.
! # [PmLink] http://www.ncbi.nlm.nih.gov/entrez/utils/pmlink_help.html
! end # MEDLINE
! end # Bio
Index: nbrf.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/nbrf.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** nbrf.rb 22 Feb 2006 08:43:15 -0000 1.8
--- nbrf.rb 19 Sep 2006 06:03:51 -0000 1.9
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2001-2003,2006 Naohisa Goto <ng at bioruby.org>
! # Copyright (C) 2001-2002 KATAYAMA Toshiaki <k at bioruby.org>
# License:: Ruby's
#
--- 3,7 ----
#
# Copyright:: Copyright (C) 2001-2003,2006 Naohisa Goto <ng at bioruby.org>
! # Copyright (C) 2001-2002 Toshiaki Katayama <k at bioruby.org>
# License:: Ruby's
#
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