genevalidator 1.6.2 → 1.6.3

data/aux/files/js/script.js

@@ -1,71 +0,0 @@
-//sort table
-$(function(){
-  'use strict';
-
-  // add custom parser to make the stars column to sort according to attr.
-  $.tablesorter.addParser({
-    id: 'star_scores', // called later when init the tablesorter
-    is: function() {
-      return false; // return false so this parser is not auto detected
-    },
-    format: function(s, table, cell, cellIndex) {
-      var $cell = $(cell);
-      if (cellIndex === 1) {
-        return $cell.attr('data-score') || s;
-      }
-      return s;
-    },
-    parsed: false,
-    type: 'numeric' // Setting type of data...
-  });
-
-  $('table').tablesorter({
-    headers: {
-      1 : { sorter: 'star_scores' } // Telling it to use custom parser...
-    },
-    sortList: [[0,0]],
-  });
-});
-
-
-//ToolTip
-$(function () {
-  'use strict';
-  $("[data-toggle='tooltip']").tooltip();
-});
-
-//Hide empty columns
-$(document).ready(function() {
-  'use strict';
-  if (window.chrome && (window.location.protocol === 'file:') )  {
-    $('#browseralert').modal();
-  }
-
-
-  $('#sortable_table tr th').each(function(i) {
-    //select all tds in this column
-    var tds = $(this).parents('table')
-    .find('tr td:nth-child(' + (i + 1) + ')');
-    //check if all the cells in this column are empty
-    //
-    if ($(this).hasClass('chart-column')) {
-    } else {
-      if ($(this).text().trim() === '') {
-        //hide header
-        $(this).hide();
-        //hide cells
-        tds.hide();
-      }
-    }
-  });
-});
-
-$( document ).on( "click", "td, .plot_btn", function( event ) {
-    if ($(this).hasClass('success') || $(this).hasClass('danger')){
-      var title = $(this).attr('title');
-      var val = title.replace(/[ \/]/g, '');  
-      addData(this, val);
-    } else if ($(this).hasClass('plot_btn')){
-      addData(this, 'all');
-    }
-});

data/lib/genevalidator/sequences.rb

@@ -1,101 +0,0 @@
-require 'net/http'
-require 'io/console'
-require 'yaml'
-
-module GeneValidator
-  # This is a class for the storing data on each sequence
-  class Sequence
-    attr_accessor :type # protein | mRNA
-    attr_accessor :definition
-    attr_accessor :identifier
-    attr_accessor :species
-    attr_accessor :accession_no
-    attr_accessor :length_protein
-    attr_accessor :reading_frame
-    attr_accessor :hsp_list # array of Hsp objects
-
-    attr_accessor :raw_sequence
-    attr_accessor :protein_translation # used only for nucleotides
-    attr_accessor :nucleotide_rf # used only for nucleotides
-
-    def initialize
-      @hsp_list            = []
-      @raw_sequence        = nil
-      @protein_translation = nil
-      @nucleotide_rf       = nil
-    end
-
-    def protein_translation
-      (@type == :protein) ? raw_sequence : @protein_translation
-    end
-
-    ##
-    # Gets raw sequence by fasta identifier from a fasta index file
-    # Params:
-    # +raw_seq_file+: name of the fasta file with raw sequences
-    # +index_file_name+: name of the fasta index file
-    # +identifier+: String
-    # +hash+: String - loaded content of the index file
-    # Output:
-    # String with the nucleotide sequence corresponding to the identifier
-    def get_sequence_from_index_file(raw_seq_file, index_file_name, identifier,
-                                     hash = nil)
-      hash = YAML.load_file(index_file_name) if hash.nil?
-      idx           = hash[identifier]
-      query         = IO.binread(raw_seq_file, idx[1] - idx[0], idx[0])
-      parse_query   = query.scan(/>([^\n]*)\n([A-Za-z\n]*)/)[0]
-      @raw_sequence = parse_query[1].gsub("\n", '')
-    rescue Exception
-      #   $stderr.print "Unable to retrieve raw sequence for the following" \
-      #                 "id: #{identifier}\n"
-    end
-
-    ##
-    # Gets raw sequence by accession number from a givem database
-    # Params:
-    # +accno+: accession number as String
-    # +db+: database as String
-    # Output:
-    # String with the nucleotide sequence corresponding to the accno
-    def get_sequence_by_accession_no(accno, dbtype, db)
-      if db !~ /remote/
-        blast_cmd     = "blastdbcmd -entry '#{accno}' -db '#{db}' -outfmt '%s'"
-        seq           = `#{blast_cmd}  2>&1`
-        if /Error/ =~ seq
-          fail IOError, 'GeneValidator was unable to obtain the raw sequences' \
-                        ' for the BLAST hits.'
-        end
-        @raw_sequence = seq
-      else
-        $stderr.puts "Getting sequence for '#{accno}' from NCBI - avoid this with '-r'."
-        uri = 'http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?'\
-              "db=#{dbtype}&retmax=1&usehistory=y&term=#{accno}/"
-        result = Net::HTTP.get(URI.parse(uri))
-
-        query   = result.scan(%r{<\bQueryKey\b>([\w\W\d]+)</\bQueryKey\b>})[0][0]
-        web_env = result.scan(%r{<\bWebEnv\b>([\w\W\d]+)</\bWebEnv\b>})[0][0]
-
-        uri = 'http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?'\
-              "rettype=fasta&retmode=text&retstart=0&retmax=1&db=#{dbtype}" \
-              "&query_key=#{query}&WebEnv=#{web_env}"
-        result = Net::HTTP.get(URI.parse(uri))
-
-        # parse FASTA output
-        nl            = result.index("\n")
-        seq           = result[nl + 1..-1]
-        @raw_sequence = seq.gsub!(/\n/, '')
-        @raw_sequence = '' unless @raw_sequence.index(/ERROR/).nil?
-      end
-      @raw_sequence
-    end
-
-    ##
-    # Initializes the corresponding attribute of the sequence
-    # with respect to the column name of the tabular blast output
-    def init_tabular_attribute(hash)
-      @identifier     = hash['sseqid'] if hash['sseqid']
-      @accession_no   = hash['sacc'] if hash['sacc']
-      @length_protein = hash['slen'].to_i if hash['slen']
-    end
-  end
-end