anncrsnp 0.1.0
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- checksums.yaml +7 -0
- data/.gitignore +9 -0
- data/.rspec +2 -0
- data/.travis.yml +4 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +21 -0
- data/README.md +41 -0
- data/Rakefile +6 -0
- data/anncrsnp.gemspec +35 -0
- data/bin/console +14 -0
- data/bin/grdbfinder.rb +472 -0
- data/bin/grdbmanager.rb +226 -0
- data/bin/masterfeatures.rb +188 -0
- data/bin/setup +7 -0
- data/bin/statistics.rb +193 -0
- data/database/deleteme +0 -0
- data/lib/anncrsnp/dataset.rb +178 -0
- data/lib/anncrsnp/parsers/ucscparser.rb +35 -0
- data/lib/anncrsnp/version.rb +3 -0
- data/lib/anncrsnp.rb +5 -0
- metadata +144 -0
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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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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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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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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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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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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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def length
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return @all_record.length
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end
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def first
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return @all_record.first
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end
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def last
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return @all_record.last
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end
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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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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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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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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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def empty?
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return @all_record.empty?
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end
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def get_metadata(keyword)
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return @metadata[keyword]
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end
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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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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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#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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# Footer
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output_file.puts "</body>",
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"</html>"
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output_file.close
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end
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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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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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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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puts @html_header.inspect
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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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return "<tr>#{main_header}</tr>\n<tr>#{fields_header}</tr>"
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end
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end
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require 'dataset'
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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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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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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
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data/lib/anncrsnp.rb
ADDED
metadata
ADDED
@@ -0,0 +1,144 @@
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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:
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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19
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- !ruby/object:Gem::Version
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version: '1.10'
|
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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25
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- - "~>"
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26
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- !ruby/object:Gem::Version
|
27
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version: '1.10'
|
28
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- !ruby/object:Gem::Dependency
|
29
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name: rake
|
30
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requirement: !ruby/object:Gem::Requirement
|
31
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requirements:
|
32
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+
- - "~>"
|
33
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- !ruby/object:Gem::Version
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34
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version: '10.0'
|
35
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type: :development
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36
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prerelease: false
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37
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
|
39
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+
- - "~>"
|
40
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- !ruby/object:Gem::Version
|
41
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version: '10.0'
|
42
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- !ruby/object:Gem::Dependency
|
43
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name: rspec
|
44
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requirement: !ruby/object:Gem::Requirement
|
45
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requirements:
|
46
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+
- - ">="
|
47
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+
- !ruby/object:Gem::Version
|
48
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version: '0'
|
49
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type: :development
|
50
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prerelease: false
|
51
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version_requirements: !ruby/object:Gem::Requirement
|
52
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requirements:
|
53
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+
- - ">="
|
54
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+
- !ruby/object:Gem::Version
|
55
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version: '0'
|
56
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+
- !ruby/object:Gem::Dependency
|
57
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+
name: sqlite3
|
58
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requirement: !ruby/object:Gem::Requirement
|
59
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requirements:
|
60
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+
- - ">="
|
61
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+
- !ruby/object:Gem::Version
|
62
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+
version: '0'
|
63
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type: :runtime
|
64
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+
prerelease: false
|
65
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version_requirements: !ruby/object:Gem::Requirement
|
66
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+
requirements:
|
67
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+
- - ">="
|
68
|
+
- !ruby/object:Gem::Version
|
69
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version: '0'
|
70
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+
- !ruby/object:Gem::Dependency
|
71
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name: rubyzip
|
72
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requirement: !ruby/object:Gem::Requirement
|
73
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requirements:
|
74
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+
- - ">="
|
75
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+
- !ruby/object:Gem::Version
|
76
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+
version: '0'
|
77
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+
type: :runtime
|
78
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+
prerelease: false
|
79
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version_requirements: !ruby/object:Gem::Requirement
|
80
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requirements:
|
81
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+
- - ">="
|
82
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+
- !ruby/object:Gem::Version
|
83
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version: '0'
|
84
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+
description: 'AnNCR-SNP integrates data from various sources, allowing the user to
|
85
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investigate the potential effects of variants in non-coding regions of the human
|
86
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genome. AnNCR-SNP consists of a database containing data on all non-coding elements
|
87
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and two main programs: manager and finder. The manager program is responsible for
|
88
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creating the local data-base, and the finder program receives the user queries in
|
89
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order to search in the local database and retrieve information. The user can find
|
90
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information about various regu-latory elements, such as TFBs, open chromatin, histone
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91
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modification and methyla-tion sites, information about SNPs from dbSNP and gene
|
92
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information from RefSeq.'
|
93
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email:
|
94
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+
- elenarojano@outlook.com
|
95
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+
- seoanezonjic@hotmail.com
|
96
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+
executables: []
|
97
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+
extensions: []
|
98
|
+
extra_rdoc_files: []
|
99
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+
files:
|
100
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+
- ".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
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+
- lib/anncrsnp/parsers/ucscparser.rb
|
118
|
+
- lib/anncrsnp/version.rb
|
119
|
+
homepage: ''
|
120
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+
licenses:
|
121
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+
- MIT
|
122
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+
metadata: {}
|
123
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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
|
143
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+
regions.
|
144
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+
test_files: []
|