Class: PluginKey
Overview
Author: Almudena Bocinos Rioboo
Defines the main methods that are necessary to execute PluginKey
Inherit: Plugin
Instance Attribute Summary
Attributes inherited from Plugin
Class Method Summary collapse
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.check_params(params) ⇒ Object
Returns an array with the errors due to parameters are missing.
Instance Method Summary collapse
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#exec_seq(seq, blast_query) ⇒ Object
Begins the pluginKey’s execution to warn where is a key in the sequence “seq”.
Methods inherited from Plugin
#add_plugin_stats, #add_stats, #add_text_stats, auto_setup, #can_execute?, check_param, #do_blasts, #execute, get_graph_filename, get_graph_title, graph_ignored?, ignored_graphs, #initialize, #merge_hits, #overlapX?, plot_setup, valid_graphs
Constructor Details
This class inherits a constructor from Plugin
Class Method Details
.check_params(params) ⇒ Object
Returns an array with the errors due to parameters are missing
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# File 'lib/seqtrimnext/plugins/plugin_key.rb', line 48 def self.check_params(params) errors=[] # self.check_param(errors,params,'blast_evalue_mids','Float') # self.check_param(errors,params,'blast_percent_mids','Integer') comment='sequences containing with diferent keys (barcodes) are saved to separate folders' default_value='false' params.check_param(errors,'use_independent_folder_for_each_key','String',default_value,comment) return errors end |
Instance Method Details
#exec_seq(seq, blast_query) ⇒ Object
Begins the pluginKey’s execution to warn where is a key in the sequence “seq”
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# File 'lib/seqtrimnext/plugins/plugin_key.rb', line 14 def exec_seq(seq,blast_query) $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: marking key into the sequence" # blast_table_results.inspect actions=[] key_size=0 # mid_size=0 key_beg,key_end=[0,3] key_size=4 key=seq.seq_fasta[0..3].upcase a = seq.new_action(key_beg,key_end,'ActionKey') # adds the actionKey to the sequence actions.push a #Add actions seq.add_actions(actions) if @group_by_key seq.add_file_tag(0,'key_' + key, :dir) add_stats('key_tag',key) end add_stats('key_size',key_size) # add_stats('mid_size',mid_size) end |