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Contents
require "plugin"
########################################################
# Author: Almudena Bocinos Rioboo
#
# Defines the main methods that are necessary to execute PluginKey
# Inherit: Plugin
########################################################
class PluginKey < Plugin
#Begins the pluginKey's execution to warn where is a key in the sequence "seq"
def execute(seqs)
@group_by_key=(@params.get_param('use_independent_folder_for_each_key')=='true')
seqs.each do |s|
exec_seq(s)
end
end
def exec_seq(seq)
$LOG.info "[#{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
#Returns an array with the errors due to parameters are missing
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
end
Version data entries
12 entries across 12 versions & 1 rubygems