Top Level Namespace

Defined Under Namespace

Modules: DomFun

Instance Method Summary collapse

Instance Method Details

#add_term2dictionary(dict, key, term) ⇒ Object 



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# File 'lib/DomFun/generalMethods.rb', line 78

def add_term2dictionary(dict, key, term)
	query = dict[key]
	if query.nil?
        	dict[key] = [term]
	else
		query << term
	end
end

#load_cafa_data(cafa_file) ⇒ Object 



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# File 'lib/DomFun/generalMethods.rb', line 87

def load_cafa_data(cafa_file)
	cafa_data = {}
	File.open(cafa_file).each do |line|
		line.chomp!
		next if line.include?('GO_Ont')
		cafa_info = line.split("\t")
		next unless cafa_info[1] == 'MF'
		go_term = cafa_info[4]
		gene_name = cafa_info[6]
		next if gene_name == 'NA'
		query = cafa_data[gene_name]
		if query.nil?
			cafa_data[gene_name] = [go_term]
		else
			query << go_term
		end
	end
	return cafa_data
end

#load_cath_data(file, category, meth = 'protACC') ⇒ Object 



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# File 'lib/DomFun/generalMethods.rb', line 40

def load_cath_data(file, category, meth='protACC')
	cath_data = {}
	protein2gene = {}
	gene2proteins = {}
	csv_file = CSV.read(file, { :col_sep => "\t" })
	csv_file.delete_at(0)
	csv_file.each do |protein_domains_data|
		next if protein_domains_data.empty?
		protein_id = protein_domains_data[0]
		if meth == 'protACC'
			field = 3
		elsif meth == 'geneID'
			field = 4
		end
		gene_name = protein_domains_data[field]
		next if gene_name.include?('fusion')
		gene_name = gene_name.gsub(' ', '_') if gene_name.include?(' ')
		superfamilyID = protein_domains_data[5]
		funfamID = protein_domains_data[6]
		term2save = nil
		if category == 'superfamilyID'
			term2save = superfamilyID
		elsif category == 'funfamID'
			term2save = funfamID
		end
		add_term2dictionary(cath_data, protein_id, term2save)
		protein2gene[protein_id] = gene_name if gene_name != 'NULL'
		query = gene2proteins[gene_name]
	    if query.nil?
	      	gene2proteins[gene_name] = [protein_id] if protein_id != 'NULL'
	    else
	      query << protein_id if protein_id != 'NULL'
		end
	end
	cath_proteins_number = cath_data.keys.length
	return cath_data, protein2gene, gene2proteins, cath_proteins_number
end

#load_proteins_file(file, annotation_types) ⇒ Object 



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# File 'lib/DomFun/generalMethods.rb', line 1

def load_proteins_file(file, annotation_types)
	protein_annotations = {}
	proteins_without_annotations = []
	annotation_types.each do |type| # initialize annotation hashes
		protein_annotations[type] = {}
	end
	counter = 0
	File.open(file).each do |line|
		line.chomp!
		if counter == 0
			counter += 1
			next
		end
		line.gsub!(' ', '')
		fields = line.split("\t", 4)
		protID = fields.shift
		annotation_types.each_with_index do |type, i|
			annotations = fields[i].split(/[;,]/)
			if !annotations.empty?
				if type.include?('go')
					go_annotations = []
					annotations.each do |go_term|
						go_name, go_id = go_term.split('GO:')
						go_annotations << "GO:".concat(go_id.tr(']', '')) unless go_id.nil?	
					end
					protein_annotations[type][protID] = go_annotations
				else
					protein_annotations[type][protID] = annotations
				end
			end
			if fields.count("") == 3
				proteins_without_annotations << protID
			end
		end
		counter += 1
	end
	return protein_annotations, counter, proteins_without_annotations.uniq
end