[BioRuby-cvs] bioruby/lib/bio/io ddbjxml.rb,1.9,1.10
Mitsuteru C. Nakao
nakao at pub.open-bio.org
Thu Feb 2 16:30:32 UTC 2006
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Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv1699/lib/bio/io
Modified Files:
ddbjxml.rb
Log Message:
* Updated RDoc.
Index: ddbjxml.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ddbjxml.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** ddbjxml.rb 26 Nov 2005 09:37:11 -0000 1.9
--- ddbjxml.rb 2 Feb 2006 16:30:29 -0000 1.10
***************
*** 37,41 ****
# = Bio::DDBJ::XML
#
! # Accessing the DDBJ web services at
#
# * http://xml.nig.ac.jp/
--- 37,41 ----
# = Bio::DDBJ::XML
#
! # Accessing the DDBJ web services.
#
# * http://xml.nig.ac.jp/
***************
*** 46,77 ****
BASE_URI = "http://xml.nig.ac.jp/wsdl/"
! # = Blast
#
! # BLAST Database Search
#
# * http://xml.nig.ac.jp/doc/Blast.txt
#
! # == Examples
#
! # serv = Bio::DDBJ::XML::Blast.new
! # query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"
#
! # report = serv.searchSimple('blastp', 'SWISS', query)
! # Bio::Blast::Default::Report.new(report).each_hit do |hit|
! # hit.hsps.find_all {|x| x.evalue < 0.1 }.each do |hsp|
! # p [hsps.evalue, hsps.identity, hsps.definition]
! # end
! # end
! #
! # puts serv.searchParam('tblastn', 'ddbjvrl', query, '-m 8')
#
! # == WSDL Methods
#
! # * searchSimple(program, database, query)
# Returns a blast report in the default format.
! # * searchParam(program, database, query, param)
# Blasts with param and returns a blast report.
#
! # == References
#
# * http://xml.nig.ac.jp/doc/Blast.txt
--- 46,85 ----
BASE_URI = "http://xml.nig.ac.jp/wsdl/"
! # === Description
#
! # DDBJ XML BLAST Database Search
#
# * http://xml.nig.ac.jp/doc/Blast.txt
#
! # === Examples
#
! # serv = Bio::DDBJ::XML::Blast.new
! # program = 'blastp'
! # database = 'SWISS'
! # query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"
! #
! # report = serv.searchSimple(program, database, query)
! # Bio::Blast::Default::Report.new(report).each_hit do |hit|
! # hit.hsps.find_all {|x| x.evalue < 0.1 }.each do |hsp|
! # p [hsps.evalue, hsps.identity, hsps.definition]
! # end
! # end
#
! # program = 'tblastn'
! # database = 'ddbjvrl'
! # param = '-m 8 -e 0.001'
! # puts serv.searchParam(program, database, query, param)
#
! # === WSDL Methods
#
! # ==== searchSimple(program, database, query)
! #
# Returns a blast report in the default format.
! #
! # ==== searchParam(program, database, query, param)
! #
# Blasts with param and returns a blast report.
#
! # === References
#
# * http://xml.nig.ac.jp/doc/Blast.txt
***************
*** 79,82 ****
--- 87,92 ----
class Blast < XML
SERVER_URI = BASE_URI + "Blast.wsdl"
+
+ # returns a Bio::DDBJ::XML::Blast object.
def initialize(wsdl = nil)
super(wsdl || SERVER_URI)
***************
*** 85,89 ****
! # == ClustalW
#
# Multiple seaquece alignment using ClustalW.
--- 95,99 ----
! # === ClustalW
#
# Multiple seaquece alignment using ClustalW.
***************
*** 91,95 ****
# * http://xml.nig.ac.jp/doc/ClustalW.txt
#
! # == Examples
#
# serv = Bio::DDBJ::XML::ClustalW.new
--- 101,105 ----
# * http://xml.nig.ac.jp/doc/ClustalW.txt
#
! # === Examples
#
# serv = Bio::DDBJ::XML::ClustalW.new
***************
*** 112,121 ****
# puts serv.analyzeParam(query, '-align -matrix=blosum')
#
! # == WSDL Methods
#
! # * analyzeSimple(query)
! # * analyzeParam(query, param)
#
! # == References
#
# * http://xml.nig.ac.jp/doc/ClustalW.txt
--- 122,131 ----
# puts serv.analyzeParam(query, '-align -matrix=blosum')
#
! # === WSDL Methods
#
! # ==== analyzeSimple(query)
! # ==== analyzeParam(query, param)
#
! # === References
#
# * http://xml.nig.ac.jp/doc/ClustalW.txt
***************
*** 123,126 ****
--- 133,138 ----
class ClustalW < XML
SERVER_URI = BASE_URI + "ClustalW.wsdl"
+
+ # returns a Bio::DDBJ::XML::ClustalW object.
def initialize(wsdl = nil)
super(wsdl || SERVER_URI)
***************
*** 129,133 ****
! # = DDBJ
#
# Retrieves a sequence entry from the DDBJ DNA Data Bank Japan.
--- 141,145 ----
! # == DDBJ
#
# Retrieves a sequence entry from the DDBJ DNA Data Bank Japan.
***************
*** 135,139 ****
# * http://xml.nig.ac.jp/doc/DDBJ.txt
#
! # == Examples
#
# serv = Bio::DDBJ::XML::DDBJ.new
--- 147,151 ----
# * http://xml.nig.ac.jp/doc/DDBJ.txt
#
! # === Examples
#
# serv = Bio::DDBJ::XML::DDBJ.new
***************
*** 145,158 ****
# puts serv.getRelatedFeaturesSeq('AL121903', '59000', '64000')
#
! # == WSDL Methods
#
! # * getFFEntry(accession)
! # * getXMLEntry(accession)
! # * getFeatureInfo(accession, feature)
! # * getAllFeatures(accession)
! # * getRelatedFeatures(accession, start, stop)
! # * getRelatedFeaturesSeq(accession, start, stop)
#
! # == References
#
# * http://xml.nig.ac.jp/doc/DDBJ.txt
--- 157,170 ----
# puts serv.getRelatedFeaturesSeq('AL121903', '59000', '64000')
#
! # === WSDL Methods
#
! # ==== getFFEntry(accession)
! # ==== getXMLEntry(accession)
! # ==== getFeatureInfo(accession, feature)
! # ==== getAllFeatures(accession)
! # ==== getRelatedFeatures(accession, start, stop)
! # ==== getRelatedFeaturesSeq(accession, start, stop)
#
! # === References
#
# * http://xml.nig.ac.jp/doc/DDBJ.txt
***************
*** 160,163 ****
--- 172,177 ----
class DDBJ < XML
SERVER_URI = BASE_URI + "DDBJ.wsdl"
+
+ # returns a Bio::DDBJ::XML::DDBJ object.
def initialize(wsdl = nil)
super(wsdl || SERVER_URI)
***************
*** 166,170 ****
! # = Fasta
#
# Searching database using the Fasta package.
--- 180,184 ----
! # == Fasta
#
# Searching database using the Fasta package.
***************
*** 172,176 ****
# * http://xml.nig.ac.jp/doc/Fasta.txt
#
! # == Examples
#
# serv = Bio::DDBJ::XML::Fasta.new
--- 186,190 ----
# * http://xml.nig.ac.jp/doc/Fasta.txt
#
! # === Examples
#
# serv = Bio::DDBJ::XML::Fasta.new
***************
*** 181,190 ****
# puts serv.searchParam('fastx34_t', 'PDB', query, '-n')
#
! # == WSDL Methods
#
! # * searchSimple(program, database, query)
! # * searchParam(program, database, query, param)
#
! # == References
#
# * http://xml.nig.ac.jp/doc/Fasta.txt
--- 195,204 ----
# puts serv.searchParam('fastx34_t', 'PDB', query, '-n')
#
! # === WSDL Methods
#
! # ==== searchSimple(program, database, query)
! # ==== searchParam(program, database, query, param)
#
! # === References
#
# * http://xml.nig.ac.jp/doc/Fasta.txt
***************
*** 192,195 ****
--- 206,211 ----
class Fasta < XML
SERVER_URI = BASE_URI + "Fasta.wsdl"
+
+ # returns a Bio::DDBJ::XML::Fasta object.
def initialize(wsdl = nil)
super(wsdl || SERVER_URI)
***************
*** 198,202 ****
! # = GetEntry
#
# Retrieves database entries.
--- 214,218 ----
! # == GetEntry
#
# Retrieves database entries.
***************
*** 204,208 ****
# * http://xml.nig.ac.jp/doc/GetEntry.txt
#
! # == Examples
#
# serv = Bio::DDBJ::XML::GetEntry.new
--- 220,224 ----
# * http://xml.nig.ac.jp/doc/GetEntry.txt
#
! # === Examples
#
# serv = Bio::DDBJ::XML::GetEntry.new
***************
*** 210,246 ****
# puts serv. getPDBEntry('1AAR')
#
! # == WSDL Methods
#
! # * getEntry(database, var, param1, param2)
! # * getEntry(database, var)
! # * getDDBJEntry(accession)
! # * getDDBJCONEntry(accession)
! # * getDDBJVerEntry(accession)
! # * getLocus_DDBJEntry(locus)
! # * getGene_DDBJEntry(gene)
! # * getProd_DDBJEntry(products)
! # * getPID_DDBJEntry(pid)
! # * getClone_DDBJEntry(clone)
! # * getXML_DDBJEntry(accession)
! # * getEMBLEntry(accession)
! # * getSWISSEntry(accession)
! # * getPIREntry(accession)
! # * getPRFEntry(accession)
! # * getPDBEntry(accession)
! # * getQVEntry(accession)
! # * getDADEntry(accession)
! # * getPID_DADEntry(pid)
! # * getFASTA_DDBJEntry(accession)
! # * getFASTA_DDBJCONEntry(accession)
! # * getFASTA_DDBJVerEntry(accession)
! # * getFASTA_DDBJSeqEntry(accession, start, end)
! # * getFASTA_DADEntry(accession)
! # * getFASTA_PIREntry(accession)
! # * getFASTA_SWISSEntry(accession)
! # * getFASTA_PDBEntry(accession)
! # * getFASTA_PRFEntry(accession)
! # * getFASTA_CDSEntry(accession)
#
! # == References
#
# * http://xml.nig.ac.jp/doc/GetEntry.txt
--- 226,262 ----
# puts serv. getPDBEntry('1AAR')
#
! # === WSDL Methods
#
! # ==== getEntry(database, var, param1, param2)
! # ==== getEntry(database, var)
! # ==== getDDBJEntry(accession)
! # ==== getDDBJCONEntry(accession)
! # ==== getDDBJVerEntry(accession)
! # ==== getLocus_DDBJEntry(locus)
! # ==== getGene_DDBJEntry(gene)
! # ==== getProd_DDBJEntry(products)
! # ==== getPID_DDBJEntry(pid)
! # ==== getClone_DDBJEntry(clone)
! # ==== getXML_DDBJEntry(accession)
! # ==== getEMBLEntry(accession)
! # ==== getSWISSEntry(accession)
! # ==== getPIREntry(accession)
! # ==== getPRFEntry(accession)
! # ==== getPDBEntry(accession)
! # ==== getQVEntry(accession)
! # ==== getDADEntry(accession)
! # ==== getPID_DADEntry(pid)
! # ==== getFASTA_DDBJEntry(accession)
! # ==== getFASTA_DDBJCONEntry(accession)
! # ==== getFASTA_DDBJVerEntry(accession)
! # ==== getFASTA_DDBJSeqEntry(accession, start, end)
! # ==== getFASTA_DADEntry(accession)
! # ==== getFASTA_PIREntry(accession)
! # ==== getFASTA_SWISSEntry(accession)
! # ==== getFASTA_PDBEntry(accession)
! # ==== getFASTA_PRFEntry(accession)
! # ==== getFASTA_CDSEntry(accession)
#
! # === References
#
# * http://xml.nig.ac.jp/doc/GetEntry.txt
***************
*** 248,251 ****
--- 264,269 ----
class GetEntry < XML
SERVER_URI = BASE_URI + "GetEntry.wsdl"
+
+ # returns a Bio::DDBJ::XML::GetEntry object.
def initialize(wsdl = nil)
super(wsdl || SERVER_URI)
***************
*** 254,258 ****
! # = Gib
#
# Genome Information broker
--- 272,276 ----
! # === Gib
#
# Genome Information broker
***************
*** 260,264 ****
# * http://xml.nig.ac.jp/doc/Gib.txt
#
! # == Examples
#
# serv = Bio::DDBJ::XML::Gib.new
--- 278,282 ----
# * http://xml.nig.ac.jp/doc/Gib.txt
#
! # === Examples
#
# serv = Bio::DDBJ::XML::Gib.new
***************
*** 275,293 ****
# puts serv.getFastaFile('Nost_PCC7120:pCC7120zeta', 'cdsaa')
#
! # == WSDL Methods
#
! # * getOrganismList
! # * getChIDList
! # * getOrganismNameFromChid(chid)
! # * getChIDFromOrganismName(orgName)
! # * getAccession(chid)
! # * getPieceNumber(chid)
! # * getDivision(chid)
! # * getType(chid)
! # * getFlatFile(chid)
! # * getFastaFile(chid, type)
! # * getCDS(chid)
#
! # == References
#
# * http://xml.nig.ac.jp/doc/Gib.txt
--- 293,311 ----
# puts serv.getFastaFile('Nost_PCC7120:pCC7120zeta', 'cdsaa')
#
! # === WSDL Methods
#
! # ==== getOrganismList
! # ==== getChIDList
! # ==== getOrganismNameFromChid(chid)
! # ==== getChIDFromOrganismName(orgName)
! # ==== getAccession(chid)
! # ==== getPieceNumber(chid)
! # ==== getDivision(chid)
! # ==== getType(chid)
! # ==== getFlatFile(chid)
! # ==== getFastaFile(chid, type)
! # ==== getCDS(chid)
#
! # === References
#
# * http://xml.nig.ac.jp/doc/Gib.txt
***************
*** 295,298 ****
--- 313,318 ----
class Gib < XML
SERVER_URI = BASE_URI + "Gib.wsdl"
+
+ # returns a Bio::DDBJ::XML::Gib object.
def initialize(wsdl = nil)
super(wsdl || SERVER_URI)
***************
*** 301,305 ****
! # = Gtop
#
# GTOP: Gene to protein.
--- 321,325 ----
! # === Gtop
#
# GTOP: Gene to protein.
***************
*** 307,322 ****
# * http://xml.nig.ac.jp/doc/Gtop.txt
#
! # == Examples
#
! # serv = Bio::DDBJ::XML::Gtop.new
! # puts serv.getOrganismList
! # puts serv.getMasterInfo('thrA', 'ecol0')
#
! # == WSDL Methods
#
! # * getOrganismList
! # * getMasterInfo(orfID, organism)
#
! # == References
#
# * http://xml.nig.ac.jp/doc/Gtop.txt
--- 327,342 ----
# * http://xml.nig.ac.jp/doc/Gtop.txt
#
! # === Examples
#
! # serv = Bio::DDBJ::XML::Gtop.new
! # puts serv.getOrganismList
! # puts serv.getMasterInfo('thrA', 'ecol0')
#
! # === WSDL Methods
#
! # ==== getOrganismList
! # ==== getMasterInfo(orfID, organism)
#
! # === References
#
# * http://xml.nig.ac.jp/doc/Gtop.txt
***************
*** 324,327 ****
--- 344,349 ----
class Gtop < XML
SERVER_URI = BASE_URI + "Gtop.wsdl"
+
+ # returns a Bio::DDBJ::XML::Gtop object.
def initialize(wsdl = nil)
super(wsdl || SERVER_URI)
***************
*** 330,334 ****
! # == PML
#
# Variation database
--- 352,356 ----
! # === PML
#
# Variation database
***************
*** 336,354 ****
# * http://xml.nig.ac.jp/doc/PML.txt
#
! # == Examples
#
! # serv = Bio::DDBJ::XML::PML.new
! # puts serv.getVariation('1')
#
! # == WSDL Methods
#
! # * searchVariation(field, query, order)
! # * searchVariationSimple(field, query)
! # * searchFrequency(field, query, order)
! # * searchFrequencySimple(field, query)
! # * getVariation(variation_id)
! # * getFrequency(variation_id, population_id)
#
! # == References
#
# * http://xml.nig.ac.jp/doc/PML.txt
--- 358,376 ----
# * http://xml.nig.ac.jp/doc/PML.txt
#
! # === Examples
#
! # serv = Bio::DDBJ::XML::PML.new
! # puts serv.getVariation('1')
#
! # === WSDL Methods
#
! # ==== searchVariation(field, query, order)
! # ==== searchVariationSimple(field, query)
! # ==== searchFrequency(field, query, order)
! # ==== searchFrequencySimple(field, query)
! # ==== getVariation(variation_id)
! # ==== getFrequency(variation_id, population_id)
#
! # === References
#
# * http://xml.nig.ac.jp/doc/PML.txt
***************
*** 356,359 ****
--- 378,383 ----
class PML < XML
SERVER_URI = BASE_URI + "PML.wsdl"
+
+ # returns a Bio::DDBJ::XML::PML object.
def initialize(wsdl = nil)
super(wsdl || SERVER_URI)
***************
*** 362,366 ****
! # = SRS
#
# Sequence Retrieving System
--- 386,390 ----
! # === SRS
#
# Sequence Retrieving System
***************
*** 368,383 ****
# * http://xml.nig.ac.jp/doc/SRS.txt
#
! # == Examples
#
! # serv = Bio::DDBJ::XML::SRS.new
! # puts serv.searchSimple('[pathway-des:sugar]')
! # puts serv.searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')
#
! # == WSDL Methods
#
! # * searchSimple(query)
! # * searchParam(query, param)
#
! # == Examples
#
# * http://xml.nig.ac.jp/doc/SRS.txt
--- 392,407 ----
# * http://xml.nig.ac.jp/doc/SRS.txt
#
! # === Examples
#
! # serv = Bio::DDBJ::XML::SRS.new
! # puts serv.searchSimple('[pathway-des:sugar]')
! # puts serv.searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')
#
! # === WSDL Methods
#
! # ==== searchSimple(query)
! # ==== searchParam(query, param)
#
! # === Examples
#
# * http://xml.nig.ac.jp/doc/SRS.txt
***************
*** 385,388 ****
--- 409,414 ----
class SRS < XML
SERVER_URI = BASE_URI + "SRS.wsdl"
+
+ # returns a Bio::DDBJ::XML::SRS object.
def initialize(wsdl = nil)
super(wsdl || SERVER_URI)
***************
*** 391,395 ****
! # = TxSearch
#
# Searching taxonomy information.
--- 417,421 ----
! # === TxSearch
#
# Searching taxonomy information.
***************
*** 397,421 ****
# * http://xml.nig.ac.jp/doc/TxSearch.txt
#
! # == Examples
#
! # serv = Bio::DDBJ::XML::TxSearch.new
! # puts serv.searchSimple('*coli')
! # puts serv.searchSimple('*tardigrada*')
! # puts serv.getTxId('Escherichia coli')
! # puts serv.getTxName('562')
#
! # query = ["Campylobacter coli", "Escherichia coli"].join("\n")
! # rank = ["family", "genus"].join("\n")
! # puts serv.searchLineage(query, rank, 'Bacteria')
#
! # == WSDL Methdos
#
! # * searchSimple(tx_Name)
! # * searchParam(tx_Name, tx_Clas, tx_Rank, tx_Rmax, tx_Dcls)
! # * getTxId(tx_Name)
! # * getTxName(tx_Id)
! # * searchLineage(query, ranks, superkingdom)
#
! # == References
#
# * http://xml.nig.ac.jp/doc/TxSearch.txt
--- 423,447 ----
# * http://xml.nig.ac.jp/doc/TxSearch.txt
#
! # === Examples
#
! # serv = Bio::DDBJ::XML::TxSearch.new
! # puts serv.searchSimple('*coli')
! # puts serv.searchSimple('*tardigrada*')
! # puts serv.getTxId('Escherichia coli')
! # puts serv.getTxName('562')
#
! # query = ["Campylobacter coli", "Escherichia coli"].join("\n")
! # rank = ["family", "genus"].join("\n")
! # puts serv.searchLineage(query, rank, 'Bacteria')
#
! # === WSDL Methdos
#
! # ==== searchSimple(tx_Name)
! # ==== searchParam(tx_Name, tx_Clas, tx_Rank, tx_Rmax, tx_Dcls)
! # ==== getTxId(tx_Name)
! # ==== getTxName(tx_Id)
! # ==== searchLineage(query, ranks, superkingdom)
#
! # === References
#
# * http://xml.nig.ac.jp/doc/TxSearch.txt
***************
*** 423,426 ****
--- 449,454 ----
class TxSearch < XML
SERVER_URI = BASE_URI + "TxSearch.wsdl"
+
+ # returns a Bio::DDBJ::XML::TxSearch object.
def initialize(wsdl = nil)
super(wsdl || SERVER_URI)
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