Sha256: 410074af19615a069aa31eda1a05d71e503cacad096959a7f448d405bad12ea9
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Size: 1.33 KB
Versions: 116
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Stored size: 1.33 KB
Contents
require 'rbbt'
require 'rbbt/sources/biomart'
require 'rbbt/sources/entrez'
def tsv_file(url, native, extra, options = {})
options = Misc.add_defaults options, :persist => false, :keep_empty => true
case
when Array === native
options = Misc.add_defaults options, :key => native.last
key_field = native.first
when (String === native or Integer === native)
options = Misc.add_defaults options, :key => native
key_field = nil
else
key_field = nil
end
case
when (Array === extra and Array === extra.first)
options = Misc.add_defaults options, :fields => extra.collect{|e| e.last}
fields = extra.collect{|e| e.first}
when (Array === extra and not Array === extra.first)
options = Misc.add_defaults options, :fields => extra
fields = (1..extra.length).to_a.collect{|i| "Field#{i}"}
else
fields = nil
end
tsv = TSV.open(Open.open(url), options)
tsv.key_field ||= key_field
tsv.fields ||= fields
tsv
end
def merge_entrez(data, taxs, native, fix = nil, select = nil)
entrez = Entrez.entrez2native(taxs, :fix => fix, :select => select)
entrez.key_field = "Entrez Gene ID"
entrez.fields = [native]
entrez
data.attach entrez, "Entrez Gene ID"
end
def merge_biomart(lexicon, db, native, other, match = nil)
match ||= native.first
lexicon.attach BioMart.tsv(db, native, other)
end
Version data entries
116 entries across 116 versions & 1 rubygems