[BioRuby-cvs] bioruby/lib/bio/io brdb.rb, 1.2, 1.3 das.rb, 1.7,
1.8 dbget.rb, 1.9, 1.10 flatfile.rb, 1.35, 1.36 pubmed.rb,
1.11, 1.12 registry.rb, 1.12, 1.13 sql.rb, 1.2, 1.3
Katayama Toshiaki
k at pub.open-bio.org
Wed Sep 7 21:22:14 EDT 2005
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Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv9021/lib/bio/io
Modified Files:
brdb.rb das.rb dbget.rb flatfile.rb pubmed.rb registry.rb
sql.rb
Log Message:
* expanded tab at the line head
Index: pubmed.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/pubmed.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** pubmed.rb 5 Feb 2004 12:58:57 -0000 1.11
--- pubmed.rb 8 Sep 2005 01:22:12 -0000 1.12
***************
*** 36,43 ****
result = response.body
if result =~ /#{id}\s+Error/
! raise( result )
else
! result = result.gsub("\r", "\n").squeeze("\n").gsub(/<\/?pre>/, '')
! return result
end
end
--- 36,43 ----
result = response.body
if result =~ /#{id}\s+Error/
! raise( result )
else
! result = result.gsub("\r", "\n").squeeze("\n").gsub(/<\/?pre>/, '')
! return result
end
end
***************
*** 51,58 ****
result = response.body
if result =~ /#{id}\s+Error/
! raise( result )
else
! result = result.gsub("\r", "\n").squeeze("\n").gsub(/<\/?pre>/, '')
! return result
end
end
--- 51,58 ----
result = response.body
if result =~ /#{id}\s+Error/
! raise( result )
else
! result = result.gsub("\r", "\n").squeeze("\n").gsub(/<\/?pre>/, '')
! return result
end
end
Index: registry.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/registry.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** registry.rb 15 Feb 2004 01:44:02 -0000 1.12
--- registry.rb 8 Sep 2005 01:22:12 -0000 1.13
***************
*** 39,49 ****
env_path = ENV['OBDA_SEARCH_PATH']
if env_path and env_path.size > 0
! read_env(env_path)
else
! read_local("#{ENV['HOME']}/.bioinformatics/seqdatabase.ini")
! read_local("/etc/bioinformatics/seqdatabase.ini")
! if @registry.empty?
! read_remote("http://www.open-bio.org/registry/seqdatabase.ini")
! end
end
end
--- 39,49 ----
env_path = ENV['OBDA_SEARCH_PATH']
if env_path and env_path.size > 0
! read_env(env_path)
else
! read_local("#{ENV['HOME']}/.bioinformatics/seqdatabase.ini")
! read_local("/etc/bioinformatics/seqdatabase.ini")
! if @registry.empty?
! read_remote("http://www.open-bio.org/registry/seqdatabase.ini")
! end
end
end
***************
*** 51,68 ****
def get_database(dbname)
@registry.each do |db|
! if db.database == dbname.downcase
! case db.protocol
! when 'biofetch'
! return serv_biofetch(db)
! when 'biosql'
! return serv_biosql(db)
! when 'flat', 'index-flat', 'index-berkeleydb'
! return serv_flat(db)
! when 'bsane-corba', 'biocorba'
! raise NotImplementedError
! when 'xembl'
! raise NotImplementedError
! end
! end
end
return nil
--- 51,68 ----
def get_database(dbname)
@registry.each do |db|
! if db.database == dbname.downcase
! case db.protocol
! when 'biofetch'
! return serv_biofetch(db)
! when 'biosql'
! return serv_biosql(db)
! when 'flat', 'index-flat', 'index-berkeleydb'
! return serv_flat(db)
! when 'bsane-corba', 'biocorba'
! raise NotImplementedError
! when 'xembl'
! raise NotImplementedError
! end
! end
end
return nil
***************
*** 72,76 ****
def query(dbname)
@registry.each do |db|
! return db if db.database == dbname.downcase
end
end
--- 72,76 ----
def query(dbname)
@registry.each do |db|
! return db if db.database == dbname.downcase
end
end
***************
*** 80,88 ****
def read_env(path)
path.split('+').each do |elem|
! if /:/.match(elem)
! read_remote(elem)
! else
! read_local(elem)
! end
end
end
--- 80,88 ----
def read_env(path)
path.split('+').each do |elem|
! if /:/.match(elem)
! read_remote(elem)
! else
! read_local(elem)
! end
end
end
***************
*** 90,95 ****
def read_local(file)
if File.readable?(file)
! stanza = File.open(file).read
! parse_stanza(stanza)
end
end
--- 90,95 ----
def read_local(file)
if File.readable?(file)
! stanza = File.open(file).read
! parse_stanza(stanza)
end
end
***************
*** 98,103 ****
schema, user, host, port, reg, path, = URI.split(url)
Net::HTTP.start(host, port) do |http|
! response, = http.get(path)
! parse_stanza(response.body)
end
end
--- 98,103 ----
schema, user, host, port, reg, path, = URI.split(url)
Net::HTTP.start(host, port) do |http|
! response, = http.get(path)
! parse_stanza(response.body)
end
end
***************
*** 106,122 ****
return unless stanza
if stanza[/.*/] =~ /VERSION\s*=\s*(\S+)/
! @spec_version = $1 # for internal use (may differ on each file)
! stanza[/.*/] = '' # remove VERSION line
end
stanza.each_line do |line|
! case line
! when /^\[(.*)\]/
dbname = $1.downcase
! db = Bio::Registry::DB.new($1)
! @registry.push(db)
! when /=/
! tag, value = line.chomp.split(/\s*=\s*/)
! @registry.last[tag] = value
! end
end
end
--- 106,122 ----
return unless stanza
if stanza[/.*/] =~ /VERSION\s*=\s*(\S+)/
! @spec_version = $1 # for internal use (may differ on each file)
! stanza[/.*/] = '' # remove VERSION line
end
stanza.each_line do |line|
! case line
! when /^\[(.*)\]/
dbname = $1.downcase
! db = Bio::Registry::DB.new($1)
! @registry.push(db)
! when /=/
! tag, value = line.chomp.split(/\s*=\s*/)
! @registry.last[tag] = value
! end
end
end
***************
*** 134,140 ****
case db.driver
when /mysql/i
! driver = 'Mysql'
when /pg|postgres/i
! driver = 'Pg'
when /oracle/
when /sybase/
--- 134,140 ----
case db.driver
when /mysql/i
! driver = 'Mysql'
when /pg|postgres/i
! driver = 'Pg'
when /oracle/
when /sybase/
***************
*** 168,182 ****
def initialize(dbname)
! @database = dbname
! @property = Hash.new
end
attr_reader :database
def method_missing(meth_id)
! @property[meth_id.id2name]
end
def []=(tag, value)
! @property[tag] = value
end
--- 168,182 ----
def initialize(dbname)
! @database = dbname
! @property = Hash.new
end
attr_reader :database
def method_missing(meth_id)
! @property[meth_id.id2name]
end
def []=(tag, value)
! @property[tag] = value
end
Index: brdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/brdb.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** brdb.rb 26 Jun 2002 00:12:29 -0000 1.2
--- brdb.rb 8 Sep 2005 01:22:11 -0000 1.3
***************
*** 36,41 ****
def fetch(db_table, entry_id)
DBI.connect(*@brdb) do |dbh|
! query = "select * from #{db_table} where id = ?"
! dbh.execute(query, entry_id).fetch_all
end
end
--- 36,41 ----
def fetch(db_table, entry_id)
DBI.connect(*@brdb) do |dbh|
! query = "select * from #{db_table} where id = ?"
! dbh.execute(query, entry_id).fetch_all
end
end
***************
*** 43,51 ****
def insert(db_table, values)
if values.is_a?(Array)
! values = values.map{ |x| '"' + DBI.quote(x) + '"' }.join(",")
end
DBI.connect(*@brdb) do |dbh|
! query = "insert into #{db_table} values (?);"
! dbh.execute(query, values)
end
end
--- 43,51 ----
def insert(db_table, values)
if values.is_a?(Array)
! values = values.map{ |x| '"' + DBI.quote(x) + '"' }.join(",")
end
DBI.connect(*@brdb) do |dbh|
! query = "insert into #{db_table} values (?);"
! dbh.execute(query, values)
end
end
***************
*** 53,61 ****
def update(db_table, entry_id, values)
if values.is_a?(Hash)
! values = values.to_a.map{ |k, v| "#{k}='#{DBI.quote(v)}'" }.join(',')
end
DBI.connect(*@brdb) do |dbh|
! query = "update #{db_table} set ? where id = ?"
! dbh.execute(query, values, entry_id)
end
end
--- 53,61 ----
def update(db_table, entry_id, values)
if values.is_a?(Hash)
! values = values.to_a.map{ |k, v| "#{k}='#{DBI.quote(v)}'" }.join(',')
end
DBI.connect(*@brdb) do |dbh|
! query = "update #{db_table} set ? where id = ?"
! dbh.execute(query, values, entry_id)
end
end
Index: dbget.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/dbget.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** dbget.rb 24 Aug 2004 00:05:58 -0000 1.9
--- dbget.rb 8 Sep 2005 01:22:11 -0000 1.10
***************
*** 35,41 ****
unless serv or port # if both of serv and port are nil
! if ENV["DBGET"] =~ /:/ # and ENV["DBGET"] exists
! serv, port = ENV["DBGET"].split(':')
! end
end
serv = serv ? serv : SERV
--- 35,41 ----
unless serv or port # if both of serv and port are nil
! if ENV["DBGET"] =~ /:/ # and ENV["DBGET"] exists
! serv, port = ENV["DBGET"].split(':')
! end
end
serv = serv ? serv : SERV
***************
*** 43,47 ****
if arg.empty?
! arg = "-h" # DBGET help message
end
--- 43,47 ----
if arg.empty?
! arg = "-h" # DBGET help message
end
Index: das.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/das.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** das.rb 26 Aug 2004 10:25:35 -0000 1.7
--- das.rb 8 Sep 2005 01:22:11 -0000 1.8
***************
*** 47,52 ****
dsn = DSN.new
e.elements.each do |e|
! case e.name
! when 'SOURCE'
dsn.source = e.text
dsn.source_id = e.attributes['id']
--- 47,52 ----
dsn = DSN.new
e.elements.each do |e|
! case e.name
! when 'SOURCE'
dsn.source = e.text
dsn.source_id = e.attributes['id']
***************
*** 70,85 ****
doc = REXML::Document.new(result.body)
doc.elements.each('/descendant::ENTRY_POINTS') do |e|
! entry_point.href = e.attributes['href']
! entry_point.version = e.attributes['version']
! e.elements.each do |e|
! segment = SEGMENT.new
! segment.entry_id = e.attributes['id']
! segment.start = e.attributes['start']
! segment.stop = e.attributes['stop']
! segment.stop = e.attributes['orientation']
! segment.subparts = e.attributes['subparts']
! segment.description = e.text
! entry_point.segments << segment
! end
end
entry_point
--- 70,85 ----
doc = REXML::Document.new(result.body)
doc.elements.each('/descendant::ENTRY_POINTS') do |e|
! entry_point.href = e.attributes['href']
! entry_point.version = e.attributes['version']
! e.elements.each do |e|
! segment = SEGMENT.new
! segment.entry_id = e.attributes['id']
! segment.start = e.attributes['start']
! segment.stop = e.attributes['stop']
! segment.stop = e.attributes['orientation']
! segment.subparts = e.attributes['subparts']
! segment.description = e.text
! entry_point.segments << segment
! end
end
entry_point
***************
*** 94,98 ****
opts = []
segments.each do |s|
! opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
end
query = opts.join(';')
--- 94,98 ----
opts = []
segments.each do |s|
! opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
end
query = opts.join(';')
***************
*** 101,113 ****
doc = REXML::Document.new(result.body)
doc.elements.each('/descendant::SEQUENCE') do |e|
! sequence = DNA.new
! sequence.entry_id = e.attributes['id']
! sequence.start = e.attributes['start']
! sequence.stop = e.attributes['stop']
! sequence.version = e.attributes['version']
! e.elements.each do |e|
! sequence.sequence = Bio::Sequence::NA.new(e.text)
! sequence.length = e.attributes['length'].to_i
! end
ary << sequence
end
--- 101,113 ----
doc = REXML::Document.new(result.body)
doc.elements.each('/descendant::SEQUENCE') do |e|
! sequence = DNA.new
! sequence.entry_id = e.attributes['id']
! sequence.start = e.attributes['start']
! sequence.stop = e.attributes['stop']
! sequence.version = e.attributes['version']
! e.elements.each do |e|
! sequence.sequence = Bio::Sequence::NA.new(e.text)
! sequence.length = e.attributes['length'].to_i
! end
ary << sequence
end
***************
*** 123,127 ****
opts = []
segments.each do |s|
! opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
end
query = opts.join(';')
--- 123,127 ----
opts = []
segments.each do |s|
! opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
end
query = opts.join(';')
***************
*** 130,147 ****
doc = REXML::Document.new(result.body)
doc.elements.each('/descendant::SEQUENCE') do |e|
! sequence = SEQUENCE.new
! sequence.entry_id = e.attributes['id']
! sequence.start = e.attributes['start']
! sequence.stop = e.attributes['stop']
! sequence.moltype = e.attributes['moltype']
! sequence.version = e.attributes['version']
! case sequence.moltype
! when /dna|rna/i # 'DNA', 'ssRNA', 'dsRNA'
! sequence.sequence = Bio::Sequence::NA.new(e.text)
! when /protein/i # 'Protein
! sequence.sequence = Bio::Sequence::AA.new(e.text)
! else
! sequence.sequence = e.text
! end
ary << sequence
end
--- 130,147 ----
doc = REXML::Document.new(result.body)
doc.elements.each('/descendant::SEQUENCE') do |e|
! sequence = SEQUENCE.new
! sequence.entry_id = e.attributes['id']
! sequence.start = e.attributes['start']
! sequence.stop = e.attributes['stop']
! sequence.moltype = e.attributes['moltype']
! sequence.version = e.attributes['version']
! case sequence.moltype
! when /dna|rna/i # 'DNA', 'ssRNA', 'dsRNA'
! sequence.sequence = Bio::Sequence::NA.new(e.text)
! when /protein/i # 'Protein
! sequence.sequence = Bio::Sequence::AA.new(e.text)
! else
! sequence.sequence = e.text
! end
ary << sequence
end
***************
*** 157,161 ****
opts = []
segments.each do |s|
! opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
end
query = opts.join(';')
--- 157,161 ----
opts = []
segments.each do |s|
! opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
end
query = opts.join(';')
***************
*** 164,186 ****
doc = REXML::Document.new(result.body)
doc.elements.each('/descendant::GFF') do |e|
! types.version = e.attributes['version']
! types.href = e.attributes['href']
! e.elements.each do |e|
! segment = SEGMENT.new
! segment.entry_id = e.attributes['id']
! segment.start = e.attributes['start']
! segment.stop = e.attributes['stop']
! segment.version = e.attributes['version']
! segment.label = e.attributes['label']
! e.elements.each do |e|
! t = TYPE.new
! t.entry_id = e.attributes['id']
! t.method = e.attributes['method']
! t.category = e.attributes['category']
! t.count = e.text.to_i
! segment.types << t
! end
! types.segments << segment
! end
end
types
--- 164,186 ----
doc = REXML::Document.new(result.body)
doc.elements.each('/descendant::GFF') do |e|
! types.version = e.attributes['version']
! types.href = e.attributes['href']
! e.elements.each do |e|
! segment = SEGMENT.new
! segment.entry_id = e.attributes['id']
! segment.start = e.attributes['start']
! segment.stop = e.attributes['stop']
! segment.version = e.attributes['version']
! segment.label = e.attributes['label']
! e.elements.each do |e|
! t = TYPE.new
! t.entry_id = e.attributes['id']
! t.method = e.attributes['method']
! t.category = e.attributes['category']
! t.count = e.text.to_i
! segment.types << t
! end
! types.segments << segment
! end
end
types
***************
*** 196,209 ****
opts = []
segments.each do |s|
! opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
end
if categorize
! opts << "categorize=yes" # default is 'no'
end
feature_ids.each do |fid|
! opts << "feature_id=#{fid}"
end
group_ids.each do |gid|
! opts << "group_id=#{gid}"
end
query = opts.join(';')
--- 196,209 ----
opts = []
segments.each do |s|
! opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
end
if categorize
! opts << "categorize=yes" # default is 'no'
end
feature_ids.each do |fid|
! opts << "feature_id=#{fid}"
end
group_ids.each do |gid|
! opts << "group_id=#{gid}"
end
query = opts.join(';')
***************
*** 215,294 ****
gff.href = e.attributes['href']
e.elements.each('SEGMENT') do |e|
! segment = SEGMENT.new
! segment.entry_id = e.attributes['id']
! segment.start = e.attributes['start']
! segment.stop = e.attributes['stop']
! segment.version = e.attributes['version']
! segment.label = e.attributes['label']
! e.elements.each do |e|
! feature = FEATURE.new
! feature.entry_id = e.attributes['id']
! feature.label = e.attributes['label']
! e.elements.each do |e|
! case e.name
! when 'TYPE'
! type = TYPE.new
! type.entry_id = e.attributes['id']
! type.category = e.attributes['category']
! type.reference = e.attributes['referrence']
! type.label = e.text
! feature.types << type
! when 'METHOD'
! feature.method_id = e.attributes['id']
! feature.method = e.text
! when 'START'
! feature.start = e.text
! when 'STOP', 'END'
! feature.stop = e.text
! when 'SCORE'
! feature.score = e.text
! when 'ORIENTATION'
! feature.orientation = e.text
! when 'PHASE'
! feature.phase = e.text
! when 'NOTE'
! feature.notes << e.text
! when 'LINK'
! link = LINK.new
! link.href = e.attributes['href']
! link.text = e.text
! feature.links << link
! when 'TARGET'
! target = TARGET.new
! target.entry_id = e.attributes['id']
! target.start = e.attributes['start']
! target.stop = e.attributes['stop']
! target.name = e.text
! feature.targets << target
! when 'GROUP'
! group = GROUP.new
! group.entry_id = e.attributes['id']
! group.label = e.attributes['label']
! group.type = e.attributes['type']
! e.elements.each do |e|
! case e.name
! when 'NOTE' # in GROUP
! group.notes << e.text
! when 'LINK' # in GROUP
! link = LINK.new
! link.href = e.attributes['href']
! link.text = e.text
! group.links << link
! when 'TARGET' # in GROUP
! target = TARGET.new
! target.entry_id = e.attributes['id']
! target.start = e.attributes['start']
! target.stop = e.attributes['stop']
! target.name = e.text
! group.targets << target
! end
! end
! feature.groups << group
! end
! end
! segment.features << feature
! end
! gff.segments << segment
! end
end
gff
--- 215,294 ----
gff.href = e.attributes['href']
e.elements.each('SEGMENT') do |e|
! segment = SEGMENT.new
! segment.entry_id = e.attributes['id']
! segment.start = e.attributes['start']
! segment.stop = e.attributes['stop']
! segment.version = e.attributes['version']
! segment.label = e.attributes['label']
! e.elements.each do |e|
! feature = FEATURE.new
! feature.entry_id = e.attributes['id']
! feature.label = e.attributes['label']
! e.elements.each do |e|
! case e.name
! when 'TYPE'
! type = TYPE.new
! type.entry_id = e.attributes['id']
! type.category = e.attributes['category']
! type.reference = e.attributes['referrence']
! type.label = e.text
! feature.types << type
! when 'METHOD'
! feature.method_id = e.attributes['id']
! feature.method = e.text
! when 'START'
! feature.start = e.text
! when 'STOP', 'END'
! feature.stop = e.text
! when 'SCORE'
! feature.score = e.text
! when 'ORIENTATION'
! feature.orientation = e.text
! when 'PHASE'
! feature.phase = e.text
! when 'NOTE'
! feature.notes << e.text
! when 'LINK'
! link = LINK.new
! link.href = e.attributes['href']
! link.text = e.text
! feature.links << link
! when 'TARGET'
! target = TARGET.new
! target.entry_id = e.attributes['id']
! target.start = e.attributes['start']
! target.stop = e.attributes['stop']
! target.name = e.text
! feature.targets << target
! when 'GROUP'
! group = GROUP.new
! group.entry_id = e.attributes['id']
! group.label = e.attributes['label']
! group.type = e.attributes['type']
! e.elements.each do |e|
! case e.name
! when 'NOTE' # in GROUP
! group.notes << e.text
! when 'LINK' # in GROUP
! link = LINK.new
! link.href = e.attributes['href']
! link.text = e.text
! group.links << link
! when 'TARGET' # in GROUP
! target = TARGET.new
! target.entry_id = e.attributes['id']
! target.start = e.attributes['start']
! target.stop = e.attributes['stop']
! target.name = e.text
! group.targets << target
! end
! end
! feature.groups << group
! end
! end
! segment.features << feature
! end
! gff.segments << segment
! end
end
gff
***************
*** 298,307 ****
class DSN
attr_accessor :source, :source_id, :source_version,
! :mapmaster, :description, :description_href
end
class ENTRY_POINT
def initialize
! @segments = Array.new
end
attr_reader :segments
--- 298,307 ----
class DSN
attr_accessor :source, :source_id, :source_version,
! :mapmaster, :description, :description_href
end
class ENTRY_POINT
def initialize
! @segments = Array.new
end
attr_reader :segments
***************
*** 317,335 ****
class SEGMENT
def self.region(entry_id, start, stop)
! segment = self.new
! segment.entry_id = entry_id
! segment.start = start
! segment.stop = stop
! return segment
end
def initialize
! @features = Array.new # for FEATURE
! @types = Array.new # for TYPE
end
attr_accessor :entry_id, :start, :stop, :orientation, :description,
! :subparts, # optional
! :features, :version, :label, # for FEATURE
! :types # for TYPE
end
--- 317,335 ----
class SEGMENT
def self.region(entry_id, start, stop)
! segment = self.new
! segment.entry_id = entry_id
! segment.start = start
! segment.stop = stop
! return segment
end
def initialize
! @features = Array.new # for FEATURE
! @types = Array.new # for TYPE
end
attr_accessor :entry_id, :start, :stop, :orientation, :description,
! :subparts, # optional
! :features, :version, :label, # for FEATURE
! :types # for TYPE
end
***************
*** 346,355 ****
class TYPE
attr_accessor :entry_id, :method, :category, :count,
! :reference, :label # for FEATURE
end
class GFF
def initialize
! @segments = Array.new
end
attr_reader :segments
--- 346,355 ----
class TYPE
attr_accessor :entry_id, :method, :category, :count,
! :reference, :label # for FEATURE
end
class GFF
def initialize
! @segments = Array.new
end
attr_reader :segments
***************
*** 359,370 ****
class FEATURE
def initialize
! @notes = Array.new
! @links = Array.new
! @types = Array.new
! @targets = Array.new
! @groups = Array.new
end
attr_accessor :entry_id, :label,
! :method_id, :method, :start, :stop, :score, :orientation, :phase
attr_reader :notes, :links, :types, :targets, :groups
end
--- 359,370 ----
class FEATURE
def initialize
! @notes = Array.new
! @links = Array.new
! @types = Array.new
! @targets = Array.new
! @groups = Array.new
end
attr_accessor :entry_id, :label,
! :method_id, :method, :start, :stop, :score, :orientation, :phase
attr_reader :notes, :links, :types, :targets, :groups
end
***************
*** 380,386 ****
class GROUP
def initialize
! @notes = Array.new
! @links = Array.new
! @targets = Array.new
end
attr_accessor :entry_id, :label, :type
--- 380,386 ----
class GROUP
def initialize
! @notes = Array.new
! @links = Array.new
! @targets = Array.new
end
attr_accessor :entry_id, :label, :type
Index: sql.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/sql.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** sql.rb 25 Feb 2003 15:47:47 -0000 1.2
--- sql.rb 8 Sep 2005 01:22:12 -0000 1.3
***************
*** 58,68 ****
def initialize(dbh, entry)
! @dbh = dbh
! @bioentry_id = entry['bioentry_id']
! @database_id = entry['biodatabase_id']
! @entry_id = entry['display_id']
! @accession = entry['accession']
! @version = entry['entry_version']
! @division = entry['division']
end
attr_reader :accession, :division, :entry_id, :version
--- 58,68 ----
def initialize(dbh, entry)
! @dbh = dbh
! @bioentry_id = entry['bioentry_id']
! @database_id = entry['biodatabase_id']
! @entry_id = entry['display_id']
! @accession = entry['accession']
! @version = entry['entry_version']
! @division = entry['division']
end
attr_reader :accession, :division, :entry_id, :version
***************
*** 70,243 ****
def to_fasta
! if seq = seq
! return seq.to_fasta(@accession)
! end
end
def seq
! query = "select * from biosequence where bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! return unless row
! mol = row['molecule']
! seq = row['biosequence_str']
! case mol
! when /.na/i # 'dna' or 'rna'
! Bio::Sequence::NA.new(seq)
! else # 'protein'
! Bio::Sequence::AA.new(seq)
! end
end
def subseq(from, to)
! length = to - from + 1
! query = "select molecule, substring(biosequence_str, ?, ?) as subseq" +
! " from biosequence where bioentry_id = ?"
! row = @dbh.execute(query, from, length, @bioentry_id).fetch
! return unless row
! mol = row['molecule']
! seq = row['subseq']
! case mol
! when /.na/i # 'dna' or 'rna'
! Bio::Sequence::NA.new(seq)
! else # 'protein'
! Bio::Sequence::AA.new(seq)
! end
end
def features
! array = []
! query = "select * from seqfeature where bioentry_id = ?"
! @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
! next unless row
! f_id = row['seqfeature_id']
! k_id = row['seqfeature_key_id']
! s_id = row['seqfeature_source_id']
! rank = row['seqfeature_rank'].to_i - 1
! # key : type (gene, CDS, ...)
! type = feature_key(k_id)
! # source : database (EMBL/GenBank/SwissProt)
! database = feature_source(s_id)
! # location : position
! locations = feature_locations(f_id)
! # qualifier
! qualifiers = feature_qualifiers(f_id)
! # rank
! array[rank] = Bio::Feature.new(type, locations, qualifiers)
! end
! return Bio::Features.new(array)
end
def references
! array = []
! query = <<-END
! select * from bioentry_reference, reference
! where bioentry_id = ? and
! bioentry_reference.reference_id = reference.reference_id
! END
! @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
! next unless row
! hash = {
! 'start' => row['reference_start'],
! 'end' => row['reference_end'],
! 'journal' => row['reference_location'],
! 'title' => row['reference_title'],
! 'authors' => row['reference_authors'],
! 'medline' => row['reference_medline']
! }
! hash.default = ''
! rank = row['reference_rank'].to_i - 1
! array[rank] = hash
! end
! return array
end
def comment
! query = "select * from comment where bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! row ? row['comment_text'] : ''
end
def comments
! array = []
! query = "select * from comment where bioentry_id = ?"
! @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
! next unless row
! rank = row['comment_rank'].to_i - 1
! array[rank] = row['comment_text']
! end
! return array
end
def database
! query = "select * from biodatabase where biodatabase_id = ?"
! row = @dbh.execute(query, @database_id).fetch
! row ? row['name'] : ''
end
def date
! query = "select * from bioentry_date where bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! row ? row['date'] : ''
end
def dblink
! query = "select * from bioentry_direct_links where source_bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! row ? [row['dbname'], row['accession']] : []
end
def definition
! query = "select * from bioentry_description where bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! row ? row['description'] : ''
end
def keyword
! query = "select * from bioentry_keywords where bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! row ? row['keywords'] : ''
end
def taxonomy
! query = <<-END
! select full_lineage, common_name, ncbi_taxa_id
! from bioentry_taxa, taxa
! where bioentry_id = ? and bioentry_taxa.taxa_id = taxa.taxa_id
! END
! row = @dbh.execute(query, @bioentry_id).fetch
! @lineage = row ? row['full_lineage'] : ''
! @common_name = row ? row['common_name'] : ''
! @ncbi_taxa_id = row ? row['ncbi_taxa_id'] : ''
! row ? [@lineage, @common_name, @ncbi_taxa_id] : []
end
def lineage
! taxonomy unless @lineage
! return @lineage
end
def common_name
! taxonomy unless @common_name
! return @common_name
end
def ncbi_taxa_id
! taxonomy unless @ncbi_taxa_id
! return @ncbi_taxa_id
end
--- 70,243 ----
def to_fasta
! if seq = seq
! return seq.to_fasta(@accession)
! end
end
def seq
! query = "select * from biosequence where bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! return unless row
! mol = row['molecule']
! seq = row['biosequence_str']
! case mol
! when /.na/i # 'dna' or 'rna'
! Bio::Sequence::NA.new(seq)
! else # 'protein'
! Bio::Sequence::AA.new(seq)
! end
end
def subseq(from, to)
! length = to - from + 1
! query = "select molecule, substring(biosequence_str, ?, ?) as subseq" +
! " from biosequence where bioentry_id = ?"
! row = @dbh.execute(query, from, length, @bioentry_id).fetch
! return unless row
! mol = row['molecule']
! seq = row['subseq']
! case mol
! when /.na/i # 'dna' or 'rna'
! Bio::Sequence::NA.new(seq)
! else # 'protein'
! Bio::Sequence::AA.new(seq)
! end
end
def features
! array = []
! query = "select * from seqfeature where bioentry_id = ?"
! @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
! next unless row
! f_id = row['seqfeature_id']
! k_id = row['seqfeature_key_id']
! s_id = row['seqfeature_source_id']
! rank = row['seqfeature_rank'].to_i - 1
! # key : type (gene, CDS, ...)
! type = feature_key(k_id)
! # source : database (EMBL/GenBank/SwissProt)
! database = feature_source(s_id)
! # location : position
! locations = feature_locations(f_id)
! # qualifier
! qualifiers = feature_qualifiers(f_id)
! # rank
! array[rank] = Bio::Feature.new(type, locations, qualifiers)
! end
! return Bio::Features.new(array)
end
def references
! array = []
! query = <<-END
! select * from bioentry_reference, reference
! where bioentry_id = ? and
! bioentry_reference.reference_id = reference.reference_id
! END
! @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
! next unless row
! hash = {
! 'start' => row['reference_start'],
! 'end' => row['reference_end'],
! 'journal' => row['reference_location'],
! 'title' => row['reference_title'],
! 'authors' => row['reference_authors'],
! 'medline' => row['reference_medline']
! }
! hash.default = ''
! rank = row['reference_rank'].to_i - 1
! array[rank] = hash
! end
! return array
end
def comment
! query = "select * from comment where bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! row ? row['comment_text'] : ''
end
def comments
! array = []
! query = "select * from comment where bioentry_id = ?"
! @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
! next unless row
! rank = row['comment_rank'].to_i - 1
! array[rank] = row['comment_text']
! end
! return array
end
def database
! query = "select * from biodatabase where biodatabase_id = ?"
! row = @dbh.execute(query, @database_id).fetch
! row ? row['name'] : ''
end
def date
! query = "select * from bioentry_date where bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! row ? row['date'] : ''
end
def dblink
! query = "select * from bioentry_direct_links where source_bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! row ? [row['dbname'], row['accession']] : []
end
def definition
! query = "select * from bioentry_description where bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! row ? row['description'] : ''
end
def keyword
! query = "select * from bioentry_keywords where bioentry_id = ?"
! row = @dbh.execute(query, @bioentry_id).fetch
! row ? row['keywords'] : ''
end
def taxonomy
! query = <<-END
! select full_lineage, common_name, ncbi_taxa_id
! from bioentry_taxa, taxa
! where bioentry_id = ? and bioentry_taxa.taxa_id = taxa.taxa_id
! END
! row = @dbh.execute(query, @bioentry_id).fetch
! @lineage = row ? row['full_lineage'] : ''
! @common_name = row ? row['common_name'] : ''
! @ncbi_taxa_id = row ? row['ncbi_taxa_id'] : ''
! row ? [@lineage, @common_name, @ncbi_taxa_id] : []
end
def lineage
! taxonomy unless @lineage
! return @lineage
end
def common_name
! taxonomy unless @common_name
! return @common_name
end
def ncbi_taxa_id
! taxonomy unless @ncbi_taxa_id
! return @ncbi_taxa_id
end
***************
*** 246,315 ****
def feature_key(k_id)
! query = "select * from seqfeature_key where seqfeature_key_id = ?"
! row = @dbh.execute(query, k_id).fetch
! row ? row['key_name'] : ''
end
def feature_source(s_id)
! query = "select * from seqfeature_source where seqfeature_source_id = ?"
! row = @dbh.execute(query, s_id).fetch
! row ? row['source_name'] : ''
end
def feature_locations(f_id)
! locations = []
! query = "select * from seqfeature_location where seqfeature_id = ?"
! @dbh.execute(query, f_id).fetch_all.each do |row|
! next unless row
! location = Bio::Location.new
! location.strand = row['seq_strand']
! location.from = row['seq_start']
! location.to = row['seq_end']
! xref = feature_locations_remote(row['seqfeature_location_id'])
! location.xref_id = xref.shift unless xref.empty?
! # just omit fuzzy location for now...
! #feature_locations_qv(row['seqfeature_location_id'])
! rank = row['location_rank'].to_i - 1
! locations[rank] = location
! end
! return Bio::Locations.new(locations)
end
def feature_locations_remote(l_id)
! query = "select * from remote_seqfeature_name where seqfeature_location_id = ?"
! row = @dbh.execute(query, l_id).fetch
! row ? [row['accession'], row['version']] : []
end
def feature_locations_qv(l_id)
! query = "select * from location_qualifier_value where seqfeature_location_id = ?"
! row = @dbh.execute(query, l_id).fetch
! row ? [row['qualifier_value'], row['slot_value']] : []
end
def feature_qualifiers(f_id)
! qualifiers = []
! query = "select * from seqfeature_qualifier_value where seqfeature_id = ?"
! @dbh.execute(query, f_id).fetch_all.each do |row|
! next unless row
! key = feature_qualifiers_key(row['seqfeature_qualifier_id'])
! value = row['qualifier_value']
! qualifier = Bio::Feature::Qualifier.new(key, value)
! rank = row['seqfeature_qualifier_rank'].to_i - 1
! qualifiers[rank] = qualifier
! end
! return qualifiers.compact # .compact is nasty hack for a while
end
def feature_qualifiers_key(q_id)
! query = "select * from seqfeature_qualifier where seqfeature_qualifier_id = ?"
! row = @dbh.execute(query, q_id).fetch
! row ? row['qualifier_name'] : ''
end
end
--- 246,315 ----
def feature_key(k_id)
! query = "select * from seqfeature_key where seqfeature_key_id = ?"
! row = @dbh.execute(query, k_id).fetch
! row ? row['key_name'] : ''
end
def feature_source(s_id)
! query = "select * from seqfeature_source where seqfeature_source_id = ?"
! row = @dbh.execute(query, s_id).fetch
! row ? row['source_name'] : ''
end
def feature_locations(f_id)
! locations = []
! query = "select * from seqfeature_location where seqfeature_id = ?"
! @dbh.execute(query, f_id).fetch_all.each do |row|
! next unless row
! location = Bio::Location.new
! location.strand = row['seq_strand']
! location.from = row['seq_start']
! location.to = row['seq_end']
! xref = feature_locations_remote(row['seqfeature_location_id'])
! location.xref_id = xref.shift unless xref.empty?
! # just omit fuzzy location for now...
! #feature_locations_qv(row['seqfeature_location_id'])
! rank = row['location_rank'].to_i - 1
! locations[rank] = location
! end
! return Bio::Locations.new(locations)
end
def feature_locations_remote(l_id)
! query = "select * from remote_seqfeature_name where seqfeature_location_id = ?"
! row = @dbh.execute(query, l_id).fetch
! row ? [row['accession'], row['version']] : []
end
def feature_locations_qv(l_id)
! query = "select * from location_qualifier_value where seqfeature_location_id = ?"
! row = @dbh.execute(query, l_id).fetch
! row ? [row['qualifier_value'], row['slot_value']] : []
end
def feature_qualifiers(f_id)
! qualifiers = []
! query = "select * from seqfeature_qualifier_value where seqfeature_id = ?"
! @dbh.execute(query, f_id).fetch_all.each do |row|
! next unless row
! key = feature_qualifiers_key(row['seqfeature_qualifier_id'])
! value = row['qualifier_value']
! qualifier = Bio::Feature::Qualifier.new(key, value)
! rank = row['seqfeature_qualifier_rank'].to_i - 1
! qualifiers[rank] = qualifier
! end
! return qualifiers.compact # .compact is nasty hack for a while
end
def feature_qualifiers_key(q_id)
! query = "select * from seqfeature_qualifier where seqfeature_qualifier_id = ?"
! row = @dbh.execute(query, q_id).fetch
! row ? row['qualifier_name'] : ''
end
end
Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** flatfile.rb 10 Aug 2005 17:15:23 -0000 1.35
--- flatfile.rb 8 Sep 2005 01:22:11 -0000 1.36
***************
*** 31,35 ****
openmode = []
while x = arg[0] and !x.is_a?(Hash)
! openmode << arg.shift
end
# rest of arg: passed to FlatFile.new
--- 31,35 ----
openmode = []
while x = arg[0] and !x.is_a?(Hash)
! openmode << arg.shift
end
# rest of arg: passed to FlatFile.new
***************
*** 78,84 ****
# 1st arg: database class (or file format autodetection)
if dbclass then
! self.dbclass = dbclass
else
! autodetect
end
end
--- 78,84 ----
# 1st arg: database class (or file format autodetection)
if dbclass then
! self.dbclass = dbclass
else
! autodetect
end
end
***************
*** 89,105 ****
return nil unless @entry_raw
if raw then
! @entry_raw
else
! e = @dbclass.new(@entry_raw)
! begin
! s = e.entry_overrun
! rescue NameError
! s = nil
! end
! if s then
! @entry_raw[-(s.length), s.length] = ''
! ungets(s)
! end
! e
end
end
--- 89,105 ----
return nil unless @entry_raw
if raw then
! @entry_raw
else
! e = @dbclass.new(@entry_raw)
! begin
! s = e.entry_overrun
! rescue NameError
! s = nil
! end
! if s then
! @entry_raw[-(s.length), s.length] = ''
! ungets(s)
! end
! e
end
end
***************
*** 108,112 ****
def each_entry
while e = self.next_entry
! yield e
end
end
--- 108,112 ----
def each_entry
while e = self.next_entry
! yield e
end
end
***************
*** 135,141 ****
def eof?
if @prefetch.size > 0
! false
else
! @io.eof?
end
end
--- 135,141 ----
def eof?
if @prefetch.size > 0
! false
else
! @io.eof?
end
end
***************
*** 143,176 ****
def gets(io_rs = $/)
if @prefetch.size > 0
! if io_rs == nil then
! r = @prefetch + @io.gets(nil).to_s
! @prefetch = ''
! else
! if io_rs == '' then
! sp_rs = /\n\n/n
! sp_rs_orig = "\n\n"
! else
! sp_rs = Regexp.new(Regexp.escape(io_rs, 'n'), 0, 'n')
! sp_rs_orig = io_rs
! end
! a = @prefetch.split(sp_rs, 2)
! if a.size > 1 then
! r = a[0] + sp_rs_orig
! @prefetch = a[1]
! else
! @prefetch << @io.gets(io_rs).to_s
! a = @prefetch.split(sp_rs, 2)
! if a.size > 1 then
! r = a[0] + sp_rs_orig
! @prefetch = a[1].to_s
! else
! r = @prefetch
! @prefetch = ''
! end
! end
! end
! r
else
! @io.gets(io_rs)
end
end
--- 143,176 ----
def gets(io_rs = $/)
if @prefetch.size > 0
! if io_rs == nil then
! r = @prefetch + @io.gets(nil).to_s
! @prefetch = ''
! else
! if io_rs == '' then
! sp_rs = /\n\n/n
! sp_rs_orig = "\n\n"
! else
! sp_rs = Regexp.new(Regexp.escape(io_rs, 'n'), 0, 'n')
! sp_rs_orig = io_rs
! end
! a = @prefetch.split(sp_rs, 2)
! if a.size > 1 then
! r = a[0] + sp_rs_orig
! @prefetch = a[1]
! else
! @prefetch << @io.gets(io_rs).to_s
! a = @prefetch.split(sp_rs, 2)
! if a.size > 1 then
! r = a[0] + sp_rs_orig
! @prefetch = a[1].to_s
! else
! r = @prefetch
! @prefetch = ''
! end
! end
! end
! r
else
! @io.gets(io_rs)
end
end
***************
*** 183,190 ****
def getc
if @prefetch.size > 0 then
! r = @prefetch[0]
! @prefetch = @prefetch[1..-1]
else
! r = @io.getc
end
r
--- 183,190 ----
def getc
if @prefetch.size > 0 then
! r = @prefetch[0]
! @prefetch = @prefetch[1..-1]
else
! r = @io.getc
end
r
***************
*** 203,211 ****
def dbclass=(k)
if k then
! @dbclass = k
! @rs = @dbclass::DELIMITER
else
! @dbclass = nil
! @rs = $/
end
end
--- 203,211 ----
def dbclass=(k)
if k then
! @dbclass = k
! @rs = @dbclass::DELIMITER
else
! @dbclass = nil
! @rs = $/
end
end
***************
*** 216,229 ****
r = nil
1.upto(lines) do |x|
! if line = @io.gets then
! @prefetch << line
! if line and line.strip.size > 0 then
! r = self.class.autodetect(@prefetch)
! if r then
! self.dbclass = r
! return r
! end
! end
! end
end
self.dbclass = nil unless dbclass
--- 216,229 ----
r = nil
1.upto(lines) do |x|
! if line = @io.gets then
! @prefetch << line
! if line and line.strip.size > 0 then
! r = self.class.autodetect(@prefetch)
! if r then
! self.dbclass = r
! return r
! end
! end
! end
end
self.dbclass = nil unless dbclass
***************
*** 248,309 ****
case text
when /^LOCUS .+ bp .*[a-z]*[DR]?NA/
! Bio::GenBank
when /^LOCUS .+ aa .+/
! Bio::GenPept
when /^UI \- [0-9]+$/
! Bio::MEDLINE
!
when /^ID .+\; *(DNA|RNA|XXX)\;/
! Bio::EMBL
when /^ID .+\; *PRT\;/
! Bio::SPTR
when /^ID [-A-Za-z0-9_\.]+\; (PATTERN|RULE|MATRIX)\.$/
! Bio::PROSITE
when /^AC [-A-Za-z0-9_\.]+$/
! Bio::TRANSFAC
when /^H [-A-Z0-9_\.]+$/
! if text =~ /^M [rc]/ then
! Bio::AAindex2
! elsif text =~ /^I A\/L/ then
! Bio::AAindex1
! else
! false #fail to determine
! end
when /^CODE [0-9]+$/
! Bio::LITDB
when /^Entry [A-Z0-9]+/
! Bio::KEGG::BRITE
!
when /^ENTRY .+ KO\s*$/
! Bio::KEGG::KO
when /^ENTRY .+ Glycan\s*$/
Bio::KEGG::GLYCAN
when /^ENTRY .+ (CDS|gene|.*RNA) /
! Bio::KEGG::GENES
when /^ENTRY EC [0-9\.]+$/
! Bio::KEGG::ENZYME
when /^ENTRY C[A-Za-z0-9\._]+$/
! Bio::KEGG::COMPOUND
when /^ENTRY R[A-Za-z0-9\._]+$/
! Bio::KEGG::REACTION
when /^ENTRY [a-z]+$/
! Bio::KEGG::GENOME
when /\<\!DOCTYPE\s+maxml\-(sequences|clusters)\s+SYSTEM/
! if $1 == 'clusters'
! Bio::FANTOM::MaXML::Cluster
! elsif $1 == 'sequences'
! Bio::FANTOM::MaXML::Sequence
! else
! nil #unknown
! end
when /^HEADER .{40}\d\d\-[A-Z]{3}\-\d\d [0-9A-Z]{4}/
! Bio::PDB
when /^CLUSTAL .*\(.*\).*sequence +alignment/
! Bio::ClustalW::Report
when /\<\!DOCTYPE BlastOutput PUBLIC /
--- 248,309 ----
case text
when /^LOCUS .+ bp .*[a-z]*[DR]?NA/
! Bio::GenBank
when /^LOCUS .+ aa .+/
! Bio::GenPept
when /^UI \- [0-9]+$/
! Bio::MEDLINE
!
when /^ID .+\; *(DNA|RNA|XXX)\;/
! Bio::EMBL
when /^ID .+\; *PRT\;/
! Bio::SPTR
when /^ID [-A-Za-z0-9_\.]+\; (PATTERN|RULE|MATRIX)\.$/
! Bio::PROSITE
when /^AC [-A-Za-z0-9_\.]+$/
! Bio::TRANSFAC
when /^H [-A-Z0-9_\.]+$/
! if text =~ /^M [rc]/ then
! Bio::AAindex2
! elsif text =~ /^I A\/L/ then
! Bio::AAindex1
! else
! false #fail to determine
! end
when /^CODE [0-9]+$/
! Bio::LITDB
when /^Entry [A-Z0-9]+/
! Bio::KEGG::BRITE
!
when /^ENTRY .+ KO\s*$/
! Bio::KEGG::KO
when /^ENTRY .+ Glycan\s*$/
Bio::KEGG::GLYCAN
when /^ENTRY .+ (CDS|gene|.*RNA) /
! Bio::KEGG::GENES
when /^ENTRY EC [0-9\.]+$/
! Bio::KEGG::ENZYME
when /^ENTRY C[A-Za-z0-9\._]+$/
! Bio::KEGG::COMPOUND
when /^ENTRY R[A-Za-z0-9\._]+$/
! Bio::KEGG::REACTION
when /^ENTRY [a-z]+$/
! Bio::KEGG::GENOME
when /\<\!DOCTYPE\s+maxml\-(sequences|clusters)\s+SYSTEM/
! if $1 == 'clusters'
! Bio::FANTOM::MaXML::Cluster
! elsif $1 == 'sequences'
! Bio::FANTOM::MaXML::Sequence
! else
! nil #unknown
! end
when /^HEADER .{40}\d\d\-[A-Z]{3}\-\d\d [0-9A-Z]{4}/
! Bio::PDB
when /^CLUSTAL .*\(.*\).*sequence +alignment/
! Bio::ClustalW::Report
when /\<\!DOCTYPE BlastOutput PUBLIC /
***************
*** 311,327 ****
when /^BLAST.? +[\-\.\w]+\-WashU +\[[\-\.\w ]+\]/
! Bio::Blast::WU::Report
when /^TBLAST.? +[\-\.\w]+\-WashU +\[[\-\.\w ]+\]/
! Bio::Blast::WU::Report_TBlast
when /^BLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/
! Bio::Blast::Default::Report
when /^TBLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/
! Bio::Blast::Default::Report_TBlast
when /^psLayout version \d+\s*$/
Bio::Blat::Report
when /^\-\-SPIDEY version .+\-\-$/
! Bio::Spidey::Report
when /^seq1 \= .*\, \d+ bp(\r|\r?\n)seq2 \= .*\, \d+ bp(\r|\r?\n)/
--- 311,327 ----
when /^BLAST.? +[\-\.\w]+\-WashU +\[[\-\.\w ]+\]/
! Bio::Blast::WU::Report
when /^TBLAST.? +[\-\.\w]+\-WashU +\[[\-\.\w ]+\]/
! Bio::Blast::WU::Report_TBlast
when /^BLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/
! Bio::Blast::Default::Report
when /^TBLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/
! Bio::Blast::Default::Report_TBlast
when /^psLayout version \d+\s*$/
Bio::Blat::Report
when /^\-\-SPIDEY version .+\-\-$/
! Bio::Spidey::Report
when /^seq1 \= .*\, \d+ bp(\r|\r?\n)seq2 \= .*\, \d+ bp(\r|\r?\n)/
***************
*** 329,344 ****
when /^>.+$/
! if text =~ /^>([PF]1|[DR][LC]|N[13]|XX)\;.+/ then
! Bio::NBRF
! elsif text =~ /^>.+$\s+(^\#.*$\s*)*^\s*\d*\s*[-a-zA-Z_\.\[\]\(\)\*\+\$]+/ then
! Bio::FastaFormat
! elsif text =~ /^>.+$\s+^\s*\d+(\s+\d+)*\s*$/ then
! Bio::FastaNumericFormat
! else
! false #fail to determine
! end
else
! nil #not found
end
end
--- 329,344 ----
when /^>.+$/
! if text =~ /^>([PF]1|[DR][LC]|N[13]|XX)\;.+/ then
! Bio::NBRF
! elsif text =~ /^>.+$\s+(^\#.*$\s*)*^\s*\d*\s*[-a-zA-Z_\.\[\]\(\)\*\+\$]+/ then
! Bio::FastaFormat
! elsif text =~ /^>.+$\s+^\s*\d+(\s+\d+)*\s*$/ then
! Bio::FastaNumericFormat
! else
! false #fail to determine
! end
else
! nil #not found
end
end
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