Class: Plugin

Inherits:
Object
  • Object
show all
Defined in:
lib/seqtrimnext/plugins/plugin.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(seq, params) ⇒ Plugin

Loads the plugin’s execution whit the sequence “seq”



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 18

def initialize(seq, params)
  @params = params
  @stats ={}
  
  if can_execute?
    t1=Time.now
    execute(seq)
    t2=Time.now

    add_plugin_stats('execution_time','total_seconds',t2-t1)
  end
  
end

Instance Attribute Details

#stats ⇒ Object

Returns the value of attribute stats.



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 15

def stats
  @stats
end

Class Method Details

.auto_setup(stats_value, stats_name, x, y) ⇒ Object

automatically setup data



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 256

def self.auto_setup(stats_value,stats_name,x,y)

  # res =false
  #
  # if !self.ignored_graphs.include?(stats_name) && (self.valid_graphs.empty? || self.valid_graphs.include?(stats_name))
  #
  #   res = true
  contains_strings=false

  stats_value.keys.each do |v|
    begin
      r=Integer(v)
    rescue
      contains_strings=true
      break
    end
  end

  # puts "#{stats_name} => #{contains_strings}"


  if !contains_strings
    stats_value.keys.each do |v|
      x.push v.to_i
    end

    x.sort!

    x.each do |v|
      y.push stats_value[v.to_s].to_i
    end

  else # there are strings in X
    x2=[]

    stats_value.keys.each do |v|
      x.push "\"#{v.gsub('\"','').gsub('\'','')}\""
      x2.push v
    end

    # puts ".#{x}."
    x2.each do |v|
      # puts ".#{v}."
      y.push stats_value[v.to_s]
    end
  end

  # return res
end

.check_param(errors, params, param, param_class, default_value = nil, comment = nil) ⇒ Object

def check_length_inserted(p_start,p_end,seq_fasta_length)

min_insert_size  = @params.get_param('min_insert_size ').to_i
 v1= p_end.to_i
 v2= p_start.to_i
 v3= v1 - v2
 $LOG.debug "------ #{v3} ----"

 res = true
 if ((v1 - v2 + 1) > (seq_fasta_length  - min_insert_size ))
   $LOG.debug "ERROR------ SEQUENCE IS NOT GOOD ----"
   res = false
 end
 return res

end

search a key into the sequence Used: in class PluginLinker and PluginMid

def search_key (seq,key_start,key_end)

p_q_beg=0
p_q_end=0
if (seq.seq_fasta[key_start..key_end]==@params.get_param('key'))
   actions=[]
   #Add ActionKey and apply it to cut the sequence

   type = "ActionKey"

   p_q_beg,p_q_end=key_start,key_end
   a = seq.new_action(p_q_beg,p_q_end,type) # adds the actionKey/actionMid to the sequence

   actions.push a

   seq.add_actions(actions)  #apply cut to the sequence with the actions
 end
 return [p_q_beg,p_q_end]

end



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 204

def self.check_param(errors,params,param,param_class,default_value=nil, comment=nil)

  if !params.exists?(param)
    if !default_value.nil?
      params.set_param(param,default_value,comment)
    else
      errors.push "The param #{param} is required and thre is no default value available"
    end
  else
    s = params.get_param(param)
    # check_class=Object.const_get(param_class)
    begin
      case param_class
      when 'Integer'
        r = Integer(s)
      when 'Float'
        r = Float(s)
      when 'String'
        r = String(s)
      end

    rescue
      errors.push " The param #{param} is not a valid #{param_class}: ##{s}#"
    end
  end

end

.check_params(params) ⇒ Object

Returns an array with the errors due to parameters are missing



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 235

def self.check_params(params)
  return []
end

.get_graph_filename(plugin_name, stats_name) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 310

def self.get_graph_filename(plugin_name,stats_name)
  return (plugin_name+ '_' +stats_name)
end

.get_graph_title(plugin_name, stats_name) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 306

def self.get_graph_title(plugin_name,stats_name)
  return plugin_name + '/' +stats_name
end

.graph_ignored?(stats_name) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/seqtrimnext/plugins/plugin.rb', line 240

def self.graph_ignored?(stats_name)
  res = true

  if !self.ignored_graphs.include?(stats_name) && (self.valid_graphs.empty? || self.valid_graphs.include?(stats_name))
    res = false
  end

  return res
end

.ignored_graphs ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 314

def self.ignored_graphs
  return []
end

.plot_setup(stats_value, stats_name, x, y, init_stats, plot) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 251

def self.plot_setup(stats_value,stats_name,x,y,init_stats,plot)
  return false
end

.valid_graphs ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 318

def self.valid_graphs
  return []
end

Instance Method Details

#add_plugin_stats(cat, item, elapsed_time) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 32

def add_plugin_stats(cat,item,elapsed_time)
    @stats[cat]={} if @stats[cat].nil?
    @stats[cat][item]=elapsed_time
end

#add_stats(key, value) ⇒ Object

Initializes the structure stats to the given key and value , only when it is neccesary, and increases its counter



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 82

def add_stats(key,value)

  @stats[key]={} if @stats[key].nil?

  if @stats[key][value].nil?
    @stats[key][value] = 0
  end
  @stats[key][value] += 1

  # puts "@stats #{key} #{value}=#{ @stats[key][value]}"
end

#add_text_stats(key, value, text) ⇒ Object

Initializes the structure stats to the given key and value , only when it is neccesary, and increases its counter



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 95

def add_text_stats(key,value,text)

  @stats[key]={} if @stats[key].nil?

  if @stats[key][value].nil?
    @stats[key][value] = []
  end

  @stats[key][value].push(text)

end

#can_execute? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/seqtrimnext/plugins/plugin.rb', line 37

def can_execute?
  return true
end

#do_blasts(seqs) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 77

def do_blasts(seqs)
  return []
end

#exec_seq(seq, blast_query) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 41

def exec_seq(seq,blast_query)
end

#execute(seqs) ⇒ Object

Begins the plugin’s execution whit the sequence “seq”



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 45

def execute(seqs)
  t1=Time.now
  blasts=do_blasts(seqs)
  

  if !blasts.empty?
    
    if blasts.is_a?(Array)
      queries=blasts
    else
      queries = blasts.querys
    end

    add_plugin_stats('execution_time','blast_and_parse',Time.now-t1)

    t1=Time.now
    seqs.each_with_index do |s,i|
      exec_seq(s,queries[i])
    end

  else # there is no blast

    t1=Time.now
    seqs.each do |s|
      exec_seq(s,nil)
    end
  end

  add_plugin_stats('execution_time','exec_seq',Time.now-t1)

end

#merge_hits(hits, merged_hits, merged_ids = nil, merge_different_ids = true) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin.rb', line 117

def merge_hits(hits,merged_hits,merged_ids=nil, merge_different_ids=true)
  # puts " merging ============"
  # hits.each do |hit|
  hits.sort{|h1,h2| (h1.q_end-h1.q_beg+1)<=>(h2.q_end-h2.q_beg+1)}.reverse_each do |hit|

    merged_ids.push hit.definition if !merged_ids.nil? && (! merged_ids.include?(hit.definition))
    # if new hit's position is already contained in hits, then ignore the new hit
    if merge_different_ids
      c=merged_hits.find{|c| overlapX?(hit.q_beg, hit.q_end,c.q_beg,c.q_end)}
    else
      # overlap with existent hit and same subject id
      c=merged_hits.find{|c| (overlapX?(hit.q_beg, hit.q_end,c.q_beg,c.q_end) && (hit.subject_id==c.subject_id))}
    end
    # puts " c #{c.inspect}"

    if (c.nil?)
      # add new contaminant
      #puts "NEW HIT #{hit.inspect}"
      merged_hits.push(hit.dup)
      #contaminants.push({:q_begin=>hit.q_beg,:q_end=>hit.q_end,:name=>hit.subject_id})
      #
    else

      # one is inside each other, just ignore
      if ((hit.q_beg>=c.q_beg && hit.q_end <=c.q_end) || (c.q_beg>=hit.q_beg && c.q_end <= hit.q_end))
        # puts "* #{hit.subject_id} inside #{c.subject_id}"
      else
        # merge with old contaminant
        # puts "#{hit.subject_id} NOT inside #{c.subject_id}"
        min=[c.q_beg,hit.q_beg].min
        max=[c.q_end,hit.q_end].max

        c.q_beg=min
        c.q_end=max


        # DONE para describir cada Id contaminante encontrado
        # puts "1 -#{c.subject_id}-   -#{hit.subject_id}-"
        c.subject_id += ' ' + hit.subject_id if (not c.subject_id.include?(hit.subject_id))
        # puts "2 -#{c.subject_id}-   -#{hit.subject_id}-"
        # puts "MERGE HIT (#{c.inspect})"
      end
      #
    end

  end
end

#overlapX?(r1_start, r1_end, r2_start, r2_end) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/seqtrimnext/plugins/plugin.rb', line 107

def overlapX?(r1_start,r1_end,r2_start,r2_end)
  # puts r1_start.class
  #     puts r1_end.class
  #     puts r2_start.class
  #     puts r2_end.class
  #     puts "-------"
  #puts "overlap? (#{r1_start}<=#{r2_end}) and (#{r1_end}>=#{r2_start})"
  return ((r1_start<=r2_end+1) and (r1_end>=r2_start-1) )
end