module Bio::NCBI::REST::EFetch::Methods
Public Instance Methods
Retrieve journal entries by given IDs using E-Utils (efetch).
Usage¶ ↑
Bio::NCBI::REST::EFetch.journal(21854) list = [21854, 21855] Bio::NCBI::REST::EFetch.journal(list) Bio::NCBI::REST::EFetch.journal(list, "xml") ncbi = Bio::NCBI::REST::EFetch.new ncbi.journal(list) ncbi.journal(list, "xml")
Arguments:
-
ids: list of journal entry IDs (required)
-
format: “full”, “xml”
- Returns
-
String
# File lib/bio/io/ncbirest.rb 801 def journal(ids, format = "full", hash = {}) 802 case format 803 when "xml" 804 format = "full" 805 mode = "xml" 806 else 807 mode = "text" 808 end 809 opts = { "db" => "journals", "rettype" => format, "retmode" => mode } 810 opts.update(hash) 811 Bio::NCBI::REST.efetch(ids, opts) 812 end
Retrieve nucleotide sequence entries by given IDs using E-Utils (efetch).
nucleotide = nuccore + nucest + nucgss
format (rettype):
-
native all but Gene ASN Default format for viewing sequences
-
fasta all sequence FASTA view of a sequence
-
gb NA sequence
GenBank
view for sequences -
gbc NA sequence INSDSeq structured flat file
-
gbwithparts NA sequence
GenBank
CON division with sequences -
est dbEST sequence EST Report
-
gss dbGSS sequence GSS Report
-
gp AA sequence
GenPept
view -
gpc AA sequence INSDSeq structured flat file
-
seqid all sequence Convert GIs into seqids
-
acc all sequence Convert GIs into accessions
-
chr dbSNP only SNP Chromosome Report
-
flt dbSNP only SNP Flat File report
-
rsr dbSNP only SNP RS Cluster report
-
brief dbSNP only SNP ID list
-
docset dbSNP only SNP RS summary
Usage¶ ↑
Bio::NCBI::REST::EFetch.nucleotide("123,U12345,U12345.1,gb|U12345|") list = [123, "U12345.1", "gb|U12345|"] Bio::NCBI::REST::EFetch.nucleotide(list) Bio::NCBI::REST::EFetch.nucleotide(list, "fasta") Bio::NCBI::REST::EFetch.nucleotide(list, "acc") Bio::NCBI::REST::EFetch.nucleotide(list, "xml") Bio::NCBI::REST::EFetch.nucleotide("AE009950") Bio::NCBI::REST::EFetch.nucleotide("AE009950", "gbwithparts") ncbi = Bio::NCBI::REST::EFetch.new ncbi.nucleotide("123,U12345,U12345.1,gb|U12345|") ncbi.nucleotide(list) ncbi.nucleotide(list, "fasta") ncbi.nucleotide(list, "acc") ncbi.nucleotide(list, "xml") ncbi.nucleotide("AE009950") ncbi.nucleotide("AE009950", "gbwithparts")
Arguments:
-
ids: list of
NCBI
entry IDs (required) -
format: “gb”, “gbc”, “fasta”, “acc”, “xml” etc.
- Returns
-
String
# File lib/bio/io/ncbirest.rb 635 def nucleotide(ids, format = "gb", hash = {}) 636 case format 637 when "xml" 638 format = "gbc" 639 end 640 opts = { "db" => "nucleotide", "rettype" => format } 641 opts.update(hash) 642 Bio::NCBI::REST.efetch(ids, opts) 643 end
Retrieve OMIM entries by given IDs using E-Utils (efetch).
Usage¶ ↑
Bio::NCBI::REST::EFetch.omim(143100) list = [143100, 602260] Bio::NCBI::REST::EFetch.omim(list) Bio::NCBI::REST::EFetch.omim(list, "xml") ncbi = Bio::NCBI::REST::EFetch.new ncbi.omim(list) ncbi.omim(list, "xml")
Arguments:
-
ids: list of OMIM entry IDs (required)
-
format: “docsum”, “synopsis”, “variants”, “detailed”, “linkout”, “xml”
- Returns
-
String
# File lib/bio/io/ncbirest.rb 836 def omim(ids, format = "detailed", hash = {}) 837 case format 838 when "xml" 839 format = "full" 840 mode = "xml" 841 when "linkout" 842 format = "ExternalLink" 843 mode = "text" 844 else 845 mode = "text" 846 end 847 opts = { "db" => "omim", "rettype" => format, "retmode" => mode } 848 opts.update(hash) 849 Bio::NCBI::REST.efetch(ids, opts) 850 end
Retrieve PubMed
Central entries by given IDs using E-Utils (efetch).
Usage¶ ↑
Bio::NCBI::REST::EFetch.pmc(1360101) Bio::NCBI::REST::EFetch.pmc("1360101,534663") list = [1360101, 534663] Bio::NCBI::REST::EFetch.pmc(list) Bio::NCBI::REST::EFetch.pmc(list, "xml") ncbi = Bio::NCBI::REST::EFetch.new ncbi.pmc(list) ncbi.pmc(list, "xml")
Arguments:
-
ids: list of
PubMed
Central entry IDs (required) -
format: “docsum”, “xml”
- Returns
-
String
# File lib/bio/io/ncbirest.rb 767 def pmc(ids, format = "docsum", hash = {}) 768 case format 769 when "xml" 770 format = "medline" 771 mode = "xml" 772 else 773 mode = "text" 774 end 775 opts = { "db" => "pmc", "rettype" => format, "retmode" => mode } 776 Bio::NCBI::REST.efetch(ids, opts) 777 end
Retrieve protein sequence entries by given IDs using E-Utils (efetch).
protein
format (rettype):
-
native all but Gene ASN Default format for viewing sequences
-
fasta all sequence FASTA view of a sequence
-
gb NA sequence
GenBank
view for sequences -
gbc NA sequence INSDSeq structured flat file
-
gbwithparts NA sequence
GenBank
CON division with sequences -
est dbEST sequence EST Report
-
gss dbGSS sequence GSS Report
-
gp AA sequence
GenPept
view -
gpc AA sequence INSDSeq structured flat file
-
seqid all sequence Convert GIs into seqids
-
acc all sequence Convert GIs into accessions
-
chr dbSNP only SNP Chromosome Report
-
flt dbSNP only SNP Flat File report
-
rsr dbSNP only SNP RS Cluster report
-
brief dbSNP only SNP ID list
-
docset dbSNP only SNP RS summary
Usage¶ ↑
Bio::NCBI::REST::EFetch.protein("7527480,AAF63163.1,AAF63163") list = [ 7527480, "AAF63163.1", "AAF63163"] Bio::NCBI::REST::EFetch.protein(list) Bio::NCBI::REST::EFetch.protein(list, "fasta") Bio::NCBI::REST::EFetch.protein(list, "acc") Bio::NCBI::REST::EFetch.protein(list, "xml") ncbi = Bio::NCBI::REST::EFetch.new ncbi.protein("7527480,AAF63163.1,AAF63163") ncbi.protein(list) ncbi.protein(list, "fasta") ncbi.protein(list, "acc") ncbi.protein(list, "xml")
Arguments:
-
ids: list of
NCBI
entry IDs (required) -
format: “gp”, “gpc”, “fasta”, “acc”, “xml” etc.
- Returns
-
String
# File lib/bio/io/ncbirest.rb 692 def protein(ids, format = "gp", hash = {}) 693 case format 694 when "xml" 695 format = "gpc" 696 end 697 opts = { "db" => "protein", "rettype" => format } 698 opts.update(hash) 699 Bio::NCBI::REST.efetch(ids, opts) 700 end
Retrieve PubMed
entries by given IDs using E-Utils (efetch).
Usage¶ ↑
Bio::NCBI::REST::EFetch.pubmed(15496913) Bio::NCBI::REST::EFetch.pubmed("15496913,11181995") list = [15496913, 11181995] Bio::NCBI::REST::EFetch.pubmed(list) Bio::NCBI::REST::EFetch.pubmed(list, "abstract") Bio::NCBI::REST::EFetch.pubmed(list, "citation") Bio::NCBI::REST::EFetch.pubmed(list, "medline") Bio::NCBI::REST::EFetch.pubmed(list, "xml") ncbi = Bio::NCBI::REST::EFetch.new ncbi.pubmed(list) ncbi.pubmed(list, "abstract") ncbi.pubmed(list, "citation") ncbi.pubmed(list, "medline") ncbi.pubmed(list, "xml")
Arguments:
-
ids: list of
PubMed
entry IDs (required) -
format: “abstract”, “citation”, “medline”, “xml”
- Returns
-
String
# File lib/bio/io/ncbirest.rb 731 def pubmed(ids, format = "medline", hash = {}) 732 case format 733 when "xml" 734 format = "medline" 735 mode = "xml" 736 else 737 mode = "text" 738 end 739 opts = { "db" => "pubmed", "rettype" => format, "retmode" => mode } 740 opts.update(hash) 741 Bio::NCBI::REST.efetch(ids, opts) 742 end
Retrieve sequence entries by given IDs using E-Utils (efetch).
sequences = gene + genome + nucleotide + protein + popset + snp nucleotide = nuccore + nucest + nucgss
format (rettype):
-
native all but Gene ASN Default format for viewing sequences
-
fasta all sequence FASTA view of a sequence
-
gb NA sequence
GenBank
view for sequences -
gbc NA sequence INSDSeq structured flat file
-
gbwithparts NA sequence
GenBank
CON division with sequences -
est dbEST sequence EST Report
-
gss dbGSS sequence GSS Report
-
gp AA sequence
GenPept
view -
gpc AA sequence INSDSeq structured flat file
-
seqid all sequence Convert GIs into seqids
-
acc all sequence Convert GIs into accessions
-
chr dbSNP only SNP Chromosome Report
-
flt dbSNP only SNP Flat File report
-
rsr dbSNP only SNP RS Cluster report
-
brief dbSNP only SNP ID list
-
docset dbSNP only SNP RS summary
Usage¶ ↑
Bio::NCBI::REST::EFetch.sequence("123,U12345,U12345.1,gb|U12345|") list = [123, "U12345.1", "gb|U12345|"] Bio::NCBI::REST::EFetch.sequence(list) Bio::NCBI::REST::EFetch.sequence(list, "fasta") Bio::NCBI::REST::EFetch.sequence(list, "acc") Bio::NCBI::REST::EFetch.sequence(list, "xml") Bio::NCBI::REST::EFetch.sequence("AE009950") Bio::NCBI::REST::EFetch.sequence("AE009950", "gbwithparts") ncbi = Bio::NCBI::REST::EFetch.new ncbi.sequence("123,U12345,U12345.1,gb|U12345|") ncbi.sequence(list) ncbi.sequence(list, "fasta") ncbi.sequence(list, "acc") ncbi.sequence(list, "xml") ncbi.sequence("AE009950") ncbi.sequence("AE009950", "gbwithparts")
Arguments:
-
ids: list of
NCBI
entry IDs (required) -
format: “gb”, “gbc”, “fasta”, “acc”, “xml” etc.
- Returns
-
String
# File lib/bio/io/ncbirest.rb 573 def sequence(ids, format = "gb", hash = {}) 574 case format 575 when "xml" 576 format = "gbc" 577 end 578 opts = { "db" => "sequences", "rettype" => format } 579 opts.update(hash) 580 Bio::NCBI::REST.efetch(ids, opts) 581 end
Retrieve taxonomy entries by given IDs using E-Utils (efetch).
Usage¶ ↑
Bio::NCBI::REST::EFetch.taxonomy(42241) list = [232323, 290179, 286681] Bio::NCBI::REST::EFetch.taxonomy(list) Bio::NCBI::REST::EFetch.taxonomy(list, "xml") ncbi = Bio::NCBI::REST::EFetch.new ncbi.taxonomy(list) ncbi.taxonomy(list, "xml")
Arguments:
-
ids: list of Taxonomy entry IDs (required)
-
format: “brief”, “docsum”, “xml”
- Returns
-
String
# File lib/bio/io/ncbirest.rb 874 def taxonomy(ids, format = "docsum", hash = {}) 875 case format 876 when "xml" 877 format = "full" 878 mode = "xml" 879 else 880 mode = "text" 881 end 882 opts = { "db" => "taxonomy", "rettype" => format, "retmode" => mode } 883 Bio::NCBI::REST.efetch(ids, opts) 884 end