Module | Bio::NCBI::REST::EFetch::Methods |
In: |
lib/bio/io/ncbirest.rb
|
Retrieve journal entries by given IDs using E-Utils (efetch).
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 762 762: def journal(ids, format = "full", hash = {}) 763: case format 764: when "xml" 765: format = "full" 766: mode = "xml" 767: else 768: mode = "text" 769: end 770: opts = { "db" => "journals", "rettype" => format, "retmode" => mode } 771: opts.update(hash) 772: Bio::NCBI::REST.efetch(ids, opts) 773: end
Retrieve nucleotide sequence entries by given IDs using E-Utils (efetch).
nucleotide = nuccore + nucest + nucgss
format (rettype):
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 596 596: def nucleotide(ids, format = "gb", hash = {}) 597: case format 598: when "xml" 599: format = "gbc" 600: end 601: opts = { "db" => "nucleotide", "rettype" => format } 602: opts.update(hash) 603: Bio::NCBI::REST.efetch(ids, opts) 604: end
Retrieve OMIM entries by given IDs using E-Utils (efetch).
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 797 797: def omim(ids, format = "detailed", hash = {}) 798: case format 799: when "xml" 800: format = "full" 801: mode = "xml" 802: when "linkout" 803: format = "ExternalLink" 804: mode = "text" 805: else 806: mode = "text" 807: end 808: opts = { "db" => "omim", "rettype" => format, "retmode" => mode } 809: opts.update(hash) 810: Bio::NCBI::REST.efetch(ids, opts) 811: end
Retrieve PubMed Central entries by given IDs using E-Utils (efetch).
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 728 728: def pmc(ids, format = "docsum", hash = {}) 729: case format 730: when "xml" 731: format = "medline" 732: mode = "xml" 733: else 734: mode = "text" 735: end 736: opts = { "db" => "pmc", "rettype" => format, "retmode" => mode } 737: Bio::NCBI::REST.efetch(ids, opts) 738: end
Retrieve protein sequence entries by given IDs using E-Utils (efetch).
protein
format (rettype):
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 653 653: def protein(ids, format = "gp", hash = {}) 654: case format 655: when "xml" 656: format = "gpc" 657: end 658: opts = { "db" => "protein", "rettype" => format } 659: opts.update(hash) 660: Bio::NCBI::REST.efetch(ids, opts) 661: end
Retrieve PubMed entries by given IDs using E-Utils (efetch).
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 692 692: def pubmed(ids, format = "medline", hash = {}) 693: case format 694: when "xml" 695: format = "medline" 696: mode = "xml" 697: else 698: mode = "text" 699: end 700: opts = { "db" => "pubmed", "rettype" => format, "retmode" => mode } 701: opts.update(hash) 702: Bio::NCBI::REST.efetch(ids, opts) 703: end
Retrieve sequence entries by given IDs using E-Utils (efetch).
sequences = gene + genome + nucleotide + protein + popset + snp nucleotide = nuccore + nucest + nucgss
format (rettype):
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 534 534: def sequence(ids, format = "gb", hash = {}) 535: case format 536: when "xml" 537: format = "gbc" 538: end 539: opts = { "db" => "sequences", "rettype" => format } 540: opts.update(hash) 541: Bio::NCBI::REST.efetch(ids, opts) 542: end
Retrieve taxonomy entries by given IDs using E-Utils (efetch).
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 835 835: def taxonomy(ids, format = "docsum", hash = {}) 836: case format 837: when "xml" 838: format = "full" 839: mode = "xml" 840: else 841: mode = "text" 842: end 843: opts = { "db" => "taxonomy", "rettype" => format, "retmode" => mode } 844: Bio::NCBI::REST.efetch(ids, opts) 845: end