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Contents
module Sinatra
module RbbtMiscHelpers
def OR_matrices(m1, m2)
samples = m1.fields
new = TSV.setup({}, :key_field => "Ensembl Gene ID", :fields => samples)
m1.each do |gene, values|
new[gene] = values
end
m2.each do |gene, values|
if new.include? gene
new[gene] = new[gene].zip(values).collect do |old, new|
case
when old == new
old
else
"TRUE"
end
end
else
new[gene] = values
end
end
new
end
def exome_bed_file_for_genes(genes)
bed = TSV.setup({}, :key_field => "Ensembl Exon ID", :fields => %w(chr start end gene), :type => :list)
organism = genes.organism
exon_info = Organism.exons(organism).tsv :fields => ["Chromosome Name", "Exon Chr Start", "Exon Chr End"], :persist => true
exons_for = Organism.exons(organism).tsv :key_field => "Ensembl Gene ID", :fields => ["Ensembl Exon ID"], :persist => true, :merge => true, :type => :flat
genes.each do |gene|
exons = exons_for[gene.ensembl]
exons.each do |exon|
chr, start, eend = exon_info[exon]
bed[exon] = [chr, start, eend, gene]
end
end
bed
end
def format_name(name)
parts = name.split("_")
hash = parts.pop
clean_name = parts * "_"
"<span class='name' jobname='#{ name }'>#{ clean_name }</span> <span class='hash'>#{ hash }</span>"
end
def values2d3(data)
data = data.to_single if data.respond_to? :to_single and not data.type == :single
values = []
data.each do |key, value|
name = key.respond_to?(:name) ? key.name || key : key
values << {:label => name, :value => value}
end
values
end
end
end
Version data entries
45 entries across 45 versions & 1 rubygems