anncrsnp 0.1.0

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Files changed (21) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +9 -0
  3. data/.rspec +2 -0
  4. data/.travis.yml +4 -0
  5. data/Gemfile +4 -0
  6. data/LICENSE.txt +21 -0
  7. data/README.md +41 -0
  8. data/Rakefile +6 -0
  9. data/anncrsnp.gemspec +35 -0
  10. data/bin/console +14 -0
  11. data/bin/grdbfinder.rb +472 -0
  12. data/bin/grdbmanager.rb +226 -0
  13. data/bin/masterfeatures.rb +188 -0
  14. data/bin/setup +7 -0
  15. data/bin/statistics.rb +193 -0
  16. data/database/deleteme +0 -0
  17. data/lib/anncrsnp/dataset.rb +178 -0
  18. data/lib/anncrsnp/parsers/ucscparser.rb +35 -0
  19. data/lib/anncrsnp/version.rb +3 -0
  20. data/lib/anncrsnp.rb +5 -0
  21. metadata +144 -0
data/lib/anncrsnp/dataset.rb ADDED
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+ CHR = 0
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+ START = 1
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+ ENDING = 2
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+ ID = 3
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+
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+ class Dataset
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+ def initialize(header = [])
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+ @all_record = []
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+ @metadata = {}
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+ add_metadata(:header, [:chr, :start, :ending, :id].concat(header))
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+ end
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+
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+ def add_record(fields_array) # Fixed col => 0 -> chr, 1 -> start, 2 -> end, 3 -> id
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+ fields_array[START] = fields_array[START].to_i
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+ fields_array[ENDING] = fields_array[ENDING].to_i
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+ @all_record << fields_array
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+ end
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+
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+ def add_record_batch(records_array)
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+ records_array.each do |record|
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+ add_record(record)
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+ end
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+ end
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+
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+ def get_elements_on_position(chr, start, ending)
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+ results = []
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+ @all_record.each do |record|
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+ if record[CHR] == chr
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+ if (record[START] >= start && record[START] <= ending) || (record[ENDING] >= start && record[ENDING] <= ending)
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+ results << record
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+ end
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+ end
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+ end
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+ return results
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+ end
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+
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+ def each_record
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+ @all_record.each do |record|
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+ yield(record)
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+ end
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+ end
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+
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+ def length
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+ return @all_record.length
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+ end
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+
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+ def first
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+ return @all_record.first
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+ end
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+
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+ def last
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+ return @all_record.last
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+ end
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+
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+ def numeric_filter(col_name, thresold)
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+ index = get_metadata(:header).index(col_name)
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+ @all_record.select!{|rec| rec[index].to_f >= thresold }
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+ end
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+
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+ def drop_columns(col_names)
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+ drop_index = col_names.map{|name| get_metadata(:header).index(name)}
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+ each_record do |rec|
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+ drop_index.reverse_each do |ind|
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+ rec.delete_at(ind)
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+ end
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+ end
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+ add_metadata(:header, get_metadata(:header) - col_names)
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+ end
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+
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+ def extract_records_by_coordinates(dataset, results_column_name)
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+ added_fields = get_metadata(:added_fields)
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+ if added_fields
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+ added_fields[results_column_name] = dataset.get_metadata(:header)
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+ else
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+ added_fields = {results_column_name => dataset.get_metadata(:header)}
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+ end
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+ add_metadata(:added_fields, added_fields)
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+ add_metadata(:header, get_metadata(:header).concat([results_column_name])) # Add new column to dataset
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+ each_record{|record|
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+
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+ record << dataset.get_elements_on_position(record[CHR], record[START], record[ENDING])
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+ }
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+ end
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+
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+ def empty?
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+ return @all_record.empty?
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+ end
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+
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+ def get_metadata(keyword)
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+ return @metadata[keyword]
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+ end
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+
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+ def add_metadata(keyword, value)
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+ return @metadata[keyword] = value
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+ end
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+
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+ def write(output_path, output_format)
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+ path = "#{output_path}.#{output_format}"
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+ if output_format == 'html'
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+ write_html(path)
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+ end
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+ end
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+ def write_html(path)
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+ output_file = File.open(path, 'w')
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+ # Header
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+ output_file.puts "<html>",
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+ "<header>",
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+ "</header>",
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+ "<body>"
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+
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+ #Table
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+ output_file.puts '<table border=1>'
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+ output_file.puts write_html_table_header
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+ each_record{|record|
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+ output_file.puts create_record_template(record)
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+ }
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+ output_file.puts "</table>"
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+
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+ # Footer
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+ output_file.puts "</body>",
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+ "</html>"
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+
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+ output_file.close
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+ end
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+
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+ def create_record_template(record)
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+ record_template = []
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+ record_lentgh = record.select{|field| field.class == Array }.map{|field| field.length}.max
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+ record_lentgh = 1 if record_lentgh.nil? || record_lentgh == 0
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+ record_lentgh.times do
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+ record_template << Array.new(@fields_number){" "}
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+ end
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+ field_position = 0
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+ record.each_with_index do |field, column_number|
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+ if field.class != Array
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+ record_template[0][field_position] = field
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+ field_position += 1
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+ else
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+ field.each_with_index do |added_record, raw|
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+ added_record.each_with_index do |record_field, col|
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+ record_template[raw][col+field_position+1] = record_field
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+ end
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+ end
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+
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+ field_position += @html_header[column_number- @html_header.first.last.length+1].last.length
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+ #field_position += @html_header[get_metadata(:header)[column_number]].length
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+ end
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+ end
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+ record_html = ""
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+ record_template.each do |row|
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+ record_html << "<tr><td>#{row.join("</td><td>")}</td></tr>\n"
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+ end
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+ return record_html
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+ end
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+
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+ def write_html_table_header
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+ @html_header = []
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+ added_fields = get_metadata(:added_fields)
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+ @html_header << [ get_metadata(:classification) , get_metadata(:header) - added_fields.keys]
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+ puts @html_header.inspect
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+ added_fields.each do |classification, fields|
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+ @html_header << [classification, fields]
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+ end
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+
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+ puts @html_header.inspect
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+
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+ main_header = ""
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+ fields_header = ""
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+ @fields_number = 0
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+ @html_header.each do |classification, fields|
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+ main_header << "<td colspan=\"#{fields.length}\">#{classification.to_s}"
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+ fields_header << "<td>#{fields.map{|h| h.to_s}.join("</td><td>")}</td>"
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+ @fields_number += fields.length
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+ end
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+
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+ return "<tr>#{main_header}</tr>\n<tr>#{fields_header}</tr>"
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+ end
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+ end
data/lib/anncrsnp/parsers/ucscparser.rb ADDED
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+ require 'dataset'
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+
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+ def parseUCSCformat(file, header, skip_first_col = TRUE)
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+ dataset = Dataset.new(header)
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+ File.open(file).each do |line|
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+ line.chomp!
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+ fields = line.split("\t")
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+ bin_signal = fields.shift if skip_first_col
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+ dataset.add_record(fields)
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+ end
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+ return dataset
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+ end
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+
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+ def parseUCSCrefseqformat(file, header, skip_first_col = TRUE)
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+ dataset = Dataset.new(header)
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+ File.open(file).each do |line|
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+ line.chomp!
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+ fields = line.split("\t")
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+ bin_signal = fields.shift if skip_first_col
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+ 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]]
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+ dataset.add_record(fields)
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+ end
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+ return dataset
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+ end
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+
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+ def parseDENdbCSVformat(file, header)
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+ dataset = Dataset.new(header)
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+ File.open(file).each do |line|
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+ line.chomp!
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+ fields = line.split(",")
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+ fields = [fields[1], fields[2], fields[3], fields[0]].concat(fields[4..11])
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+ dataset.add_record(fields)
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+ end
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+ return dataset
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+ end
data/lib/anncrsnp/version.rb ADDED
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+ module Anncrsnp
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+ VERSION = "0.1.0"
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+ end
data/lib/anncrsnp.rb ADDED
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+ require "anncrsnp/version"
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+
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+ module Anncrsnp
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+ # Your code goes here...
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: anncrsnp
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+ version: !ruby/object:Gem::Version
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+ version: 0.1.0
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+ platform: ruby
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+ authors:
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+ - Elena Rojano
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+ - Pedro Seoane
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+ autorequire:
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+ bindir: exe
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+ cert_chain: []
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+ date: 2016-01-24 00:00:00.000000000 Z
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+ dependencies:
14
+ - !ruby/object:Gem::Dependency
15
+ name: bundler
16
+ requirement: !ruby/object:Gem::Requirement
17
+ requirements:
18
+ - - "~>"
19
+ - !ruby/object:Gem::Version
20
+ version: '1.10'
21
+ type: :development
22
+ prerelease: false
23
+ version_requirements: !ruby/object:Gem::Requirement
24
+ requirements:
25
+ - - "~>"
26
+ - !ruby/object:Gem::Version
27
+ version: '1.10'
28
+ - !ruby/object:Gem::Dependency
29
+ name: rake
30
+ requirement: !ruby/object:Gem::Requirement
31
+ requirements:
32
+ - - "~>"
33
+ - !ruby/object:Gem::Version
34
+ version: '10.0'
35
+ type: :development
36
+ prerelease: false
37
+ version_requirements: !ruby/object:Gem::Requirement
38
+ requirements:
39
+ - - "~>"
40
+ - !ruby/object:Gem::Version
41
+ version: '10.0'
42
+ - !ruby/object:Gem::Dependency
43
+ name: rspec
44
+ requirement: !ruby/object:Gem::Requirement
45
+ requirements:
46
+ - - ">="
47
+ - !ruby/object:Gem::Version
48
+ version: '0'
49
+ type: :development
50
+ prerelease: false
51
+ version_requirements: !ruby/object:Gem::Requirement
52
+ requirements:
53
+ - - ">="
54
+ - !ruby/object:Gem::Version
55
+ version: '0'
56
+ - !ruby/object:Gem::Dependency
57
+ name: sqlite3
58
+ requirement: !ruby/object:Gem::Requirement
59
+ requirements:
60
+ - - ">="
61
+ - !ruby/object:Gem::Version
62
+ version: '0'
63
+ type: :runtime
64
+ prerelease: false
65
+ version_requirements: !ruby/object:Gem::Requirement
66
+ requirements:
67
+ - - ">="
68
+ - !ruby/object:Gem::Version
69
+ version: '0'
70
+ - !ruby/object:Gem::Dependency
71
+ name: rubyzip
72
+ requirement: !ruby/object:Gem::Requirement
73
+ requirements:
74
+ - - ">="
75
+ - !ruby/object:Gem::Version
76
+ version: '0'
77
+ type: :runtime
78
+ prerelease: false
79
+ version_requirements: !ruby/object:Gem::Requirement
80
+ requirements:
81
+ - - ">="
82
+ - !ruby/object:Gem::Version
83
+ version: '0'
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+ description: 'AnNCR-SNP integrates data from various sources, allowing the user to
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+ investigate the potential effects of variants in non-coding regions of the human
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+ genome. AnNCR-SNP consists of a database containing data on all non-coding elements
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+ and two main programs: manager and finder. The manager program is responsible for
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+ creating the local data-base, and the finder program receives the user queries in
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+ order to search in the local database and retrieve information. The user can find
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+ information about various regu-latory elements, such as TFBs, open chromatin, histone
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+ modification and methyla-tion sites, information about SNPs from dbSNP and gene
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+ information from RefSeq.'
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+ email:
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+ - elenarojano@outlook.com
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+ - seoanezonjic@hotmail.com
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+ executables: []
97
+ extensions: []
98
+ extra_rdoc_files: []
99
+ files:
100
+ - ".gitignore"
101
+ - ".rspec"
102
+ - ".travis.yml"
103
+ - Gemfile
104
+ - LICENSE.txt
105
+ - README.md
106
+ - Rakefile
107
+ - anncrsnp.gemspec
108
+ - bin/console
109
+ - bin/grdbfinder.rb
110
+ - bin/grdbmanager.rb
111
+ - bin/masterfeatures.rb
112
+ - bin/setup
113
+ - bin/statistics.rb
114
+ - database/deleteme
115
+ - lib/anncrsnp.rb
116
+ - lib/anncrsnp/dataset.rb
117
+ - lib/anncrsnp/parsers/ucscparser.rb
118
+ - lib/anncrsnp/version.rb
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+ homepage: ''
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+ licenses:
121
+ - MIT
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+ metadata: {}
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+ post_install_message:
124
+ rdoc_options: []
125
+ require_paths:
126
+ - lib
127
+ required_ruby_version: !ruby/object:Gem::Requirement
128
+ requirements:
129
+ - - ">="
130
+ - !ruby/object:Gem::Version
131
+ version: '0'
132
+ required_rubygems_version: !ruby/object:Gem::Requirement
133
+ requirements:
134
+ - - ">="
135
+ - !ruby/object:Gem::Version
136
+ version: '0'
137
+ requirements: []
138
+ rubyforge_project:
139
+ rubygems_version: 2.4.8
140
+ signing_key:
141
+ specification_version: 4
142
+ summary: Tool to characterize Single Nucleotide Polymorphisms (SNP) in genomic non-coding
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+ regions.
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+ test_files: []