class Object

Constants

CHR
ENDING
ID
ROOT_PATH
START

Public Instance Methods

parseDENdbCSVformat(file, header) click to toggle source
# File lib/anncrsnp/parsers/ucscparser.rb, line 26
def parseDENdbCSVformat(file, header)
        dataset = Dataset.new(header)
        File.open(file).each do |line|
                line.chomp!
                fields = line.split(",")
                fields = [fields[1], fields[2], fields[3], fields[0]].concat(fields[4..11])
                dataset.add_record(fields)
        end
        return dataset
end
parseUCSCformat(file, header, skip_first_col = TRUE, add_start = 0, add_stop = 0) click to toggle source
# File lib/anncrsnp/parsers/ucscparser.rb, line 3
def parseUCSCformat(file, header, skip_first_col = TRUE, add_start = 0, add_stop = 0)
        dataset = Dataset.new(header)
        File.open(file).each do |line|
                line.chomp!
                fields = line.split("\t") 
                bin_signal = fields.shift if skip_first_col
                dataset.add_record(fields, add_start, add_stop)
        end
        return dataset
end
parseUCSCrefseqformat(file, header, skip_first_col = TRUE, add_start = 0, add_stop = 0) click to toggle source
# File lib/anncrsnp/parsers/ucscparser.rb, line 14
def parseUCSCrefseqformat(file, header, skip_first_col = TRUE, add_start = 0, add_stop = 0)
        dataset = Dataset.new(header)
        File.open(file).each do |line|
                line.chomp!
                fields = line.split("\t") 
                bin_signal = fields.shift if skip_first_col
                fields = [fields[1], fields[3], fields[4], fields[11], fields[0], fields[2], fields[5], fields[6], fields[7], fields[8], fields[9], fields[10], fields[12], fields[13], fields[14]]
                dataset.add_record(fields, add_start, add_stop)
        end
        return dataset
end