[BioRuby-cvs] bioruby/lib/bio/io ddbjxml.rb,1.8,1.9
Mitsuteru C. Nakao
nakao at pub.open-bio.org
Sat Nov 26 04:37:13 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv27574/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 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** ddbjxml.rb 14 Nov 2005 02:01:54 -0000 1.8
--- ddbjxml.rb 26 Nov 2005 09:37:11 -0000 1.9
***************
*** 34,41 ****
--- 34,80 ----
class DDBJ
+
+ # = Bio::DDBJ::XML
+ #
+ # Accessing the DDBJ web services at
+ #
+ # * http://xml.nig.ac.jp/
+ # * http://xml.nig.ac.jp/wsdl/index.jsp
+ #
class XML < Bio::SOAPWSDL
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
+ #
class Blast < XML
SERVER_URI = BASE_URI + "Blast.wsdl"
***************
*** 45,48 ****
--- 84,124 ----
end
+
+ # == ClustalW
+ #
+ # Multiple seaquece alignment using ClustalW.
+ #
+ # * http://xml.nig.ac.jp/doc/ClustalW.txt
+ #
+ # == Examples
+ #
+ # serv = Bio::DDBJ::XML::ClustalW.new
+ #
+ # query = <<END
+ # > RABSTOUT rabbit Guinness receptor
+ # LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS
+ # ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC
+ # > MUSNOSE mouse nose drying factor
+ # mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt
+ # fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv
+ # > HSHEAVEN human Guinness receptor repeat
+ # mhkmmhkgmkhmhgmhmhg lhmkmhlkmgkhmgkmk ytytytryrwtqtqwtwyt
+ # fdgfdsgafdagfdgfsag dfavdfdvgavfsvfgv dfsvdgvagvfdv
+ # mhkmmhkgmkhmhgmhmhg lhmkmhlkmgkhmgkmk ytytytryrwtqtqwtwyt
+ # fdgfdsgafdagfdgfsag dfavdfdvgavfsvfgv dfsvdgvagvfdv
+ # END
+ #
+ # puts serv.analyzeSimple(query)
+ # puts serv.analyzeParam(query, '-align -matrix=blosum')
+ #
+ # == WSDL Methods
+ #
+ # * analyzeSimple(query)
+ # * analyzeParam(query, param)
+ #
+ # == References
+ #
+ # * http://xml.nig.ac.jp/doc/ClustalW.txt
+ #
class ClustalW < XML
SERVER_URI = BASE_URI + "ClustalW.wsdl"
***************
*** 51,55 ****
end
end
!
class DDBJ < XML
SERVER_URI = BASE_URI + "DDBJ.wsdl"
--- 127,161 ----
end
end
!
!
! # = DDBJ
! #
! # Retrieves a sequence entry from the DDBJ DNA Data Bank Japan.
! #
! # * http://xml.nig.ac.jp/doc/DDBJ.txt
! #
! # == Examples
! #
! # serv = Bio::DDBJ::XML::DDBJ.new
! # puts serv.getFFEntry('AB000050')
! # puts serv.getXMLEntry('AB000050')
! # puts serv.getFeatureInfo('AB000050', 'cds')
! # puts serv.getAllFeatures('AB000050')
! # puts serv.getRelatedFeatures('AL121903', '59000', '64000')
! # 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
! #
class DDBJ < XML
SERVER_URI = BASE_URI + "DDBJ.wsdl"
***************
*** 58,62 ****
end
end
!
class Fasta < XML
SERVER_URI = BASE_URI + "Fasta.wsdl"
--- 164,193 ----
end
end
!
!
! # = Fasta
! #
! # Searching database using the Fasta package.
! #
! # * http://xml.nig.ac.jp/doc/Fasta.txt
! #
! # == Examples
! #
! # serv = Bio::DDBJ::XML::Fasta.new
! # query = ">Test\nMSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI"
! #
! # puts serv.searchSimple('fasta34', 'PDB', query)
! # query = ">Test\nAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
! # 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
! #
class Fasta < XML
SERVER_URI = BASE_URI + "Fasta.wsdl"
***************
*** 65,69 ****
end
end
!
class GetEntry < XML
SERVER_URI = BASE_URI + "GetEntry.wsdl"
--- 196,249 ----
end
end
!
!
! # = GetEntry
! #
! # Retrieves database entries.
! #
! # * http://xml.nig.ac.jp/doc/GetEntry.txt
! #
! # == Examples
! #
! # serv = Bio::DDBJ::XML::GetEntry.new
! # puts serv.getDDBJEntry('AB000050')
! # 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
! #
class GetEntry < XML
SERVER_URI = BASE_URI + "GetEntry.wsdl"
***************
*** 72,76 ****
end
end
!
class Gib < XML
SERVER_URI = BASE_URI + "Gib.wsdl"
--- 252,296 ----
end
end
!
!
! # = Gib
! #
! # Genome Information broker
! #
! # * http://xml.nig.ac.jp/doc/Gib.txt
! #
! # == Examples
! #
! # serv = Bio::DDBJ::XML::Gib.new
! # puts serv.getOrganismList
! # puts serv.getChIDList
! # puts serv.getOrganismNameFromChid('Sent_CT18:')
! # puts serv.getChIDFromOrganismName('Aquifex aeolicus VF5')
! # puts serv.getAccession('Ecol_K12_MG1655:')
! # puts serv.getPieceNumber('Mgen_G37:')
! # puts serv.getDivision('Mgen_G37:')
! # puts serv.getType('Mgen_G37:')
! # puts serv.getCDS('Aaeo_VF5:ece1')
! # puts serv.getFlatFile('Nost_PCC7120:pCC7120zeta')
! # 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
! #
class Gib < XML
SERVER_URI = BASE_URI + "Gib.wsdl"
***************
*** 80,83 ****
--- 300,325 ----
end
+
+ # = Gtop
+ #
+ # GTOP: Gene to protein.
+ #
+ # * 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
+ #
class Gtop < XML
SERVER_URI = BASE_URI + "Gtop.wsdl"
***************
*** 87,90 ****
--- 329,357 ----
end
+
+ # == PML
+ #
+ # Variation database
+ #
+ # * 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
+ #
class PML < XML
SERVER_URI = BASE_URI + "PML.wsdl"
***************
*** 94,97 ****
--- 361,386 ----
end
+
+ # = SRS
+ #
+ # Sequence Retrieving System
+ #
+ # * 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
+ #
class SRS < XML
SERVER_URI = BASE_URI + "SRS.wsdl"
***************
*** 101,104 ****
--- 390,424 ----
end
+
+ # = TxSearch
+ #
+ # Searching taxonomy information.
+ #
+ # * 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
+ #
class TxSearch < XML
SERVER_URI = BASE_URI + "TxSearch.wsdl"
***************
*** 292,425 ****
end
-
-
-
- =begin
-
- = Bio::DDBJ::XML
-
- Accessing the DDBJ web services at
-
- * ((<URL:http://xml.nig.ac.jp/>))
- * ((<URL:http://xml.nig.ac.jp/wsdl/index.jsp>))
-
- == Blast
-
- * ((<URL:http://xml.nig.ac.jp/doc/Blast.txt>))
-
- --- searchSimple(program, database, query)
- --- searchParam(program, database, query, param)
-
- == ClustalW
-
- * ((<URL:http://xml.nig.ac.jp/doc/ClustalW.txt>))
-
- --- analyzeSimple(query)
- --- analyzeParam(query, param)
-
- == DDBJ
-
- * ((<URL:http://xml.nig.ac.jp/doc/DDBJ.txt>))
-
- --- getFFEntry(accession)
- --- getXMLEntry(accession)
- --- getFeatureInfo(accession, feature)
- --- getAllFeatures(accession)
- --- getRelatedFeatures(accession, start, stop)
- --- getRelatedFeaturesSeq(accession, start, stop)
-
- == Fasta
-
- * ((<URL:http://xml.nig.ac.jp/doc/Fasta.txt>))
-
- --- searchSimple(program, database, query)
- --- searchParam(program, database, query, param)
-
- == GetEntry
-
- * ((<URL:http://xml.nig.ac.jp/doc/GetEntry.txt>))
-
- --- 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)
-
- == Gib
-
- * ((<URL:http://xml.nig.ac.jp/doc/Gib.txt>))
-
- --- getOrganismList
- --- getChIDList
- --- getOrganismNameFromChid(chid)
- --- getChIDFromOrganismName(orgName)
- --- getAccession(chid)
- --- getPieceNumber(chid)
- --- getDivision(chid)
- --- getType(chid)
- --- getFlatFile(chid)
- --- getFastaFile(chid, type)
- --- getCDS(chid)
-
- == Gtop
-
- * ((<URL:http://xml.nig.ac.jp/doc/Gtop.txt>))
-
- --- getOrganismList
- --- getMasterInfo(orfID, organism)
-
- == PML
-
- * ((<URL:http://xml.nig.ac.jp/doc/PML.txt>))
-
- --- searchVariation(field, query, order)
- --- searchVariationSimple(field, query)
- --- searchFrequency(field, query, order)
- --- searchFrequencySimple(field, query)
- --- getVariation(variation_id)
- --- getFrequency(variation_id, population_id)
-
- == SRS
-
- * ((<URL:http://xml.nig.ac.jp/doc/SRS.txt>))
-
- --- searchSimple(query)
- --- searchParam(query, param)
-
- == TxSearch
-
- * ((<URL:http://xml.nig.ac.jp/doc/TxSearch.txt>))
-
- --- searchSimple(tx_Name)
- --- searchParam(tx_Name, tx_Clas, tx_Rank, tx_Rmax, tx_Dcls)
- --- getTxId(tx_Name)
- --- getTxName(tx_Id)
- --- searchLineage(query, ranks, superkingdom)
-
- =end
-
--- 612,614 ----
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