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Contents
require "plugin"
########################################################
# Author: Dario Guerrero
#
# Defines the main methods that are necessary to execute PluginSizeTrim
# Inherit: Plugin
# Trims the output sequences to a fixed size
########################################################
class PluginSizeTrim < Plugin
def exec_seq(seq,blast_query)
#$LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: checking if insert of sequence has enought size"
# puts "inserto #{seq.insert_start}, #{seq.insert_end} size #{seq.seq_fasta.size}"
tr_size = @params.get_param('trim_size_file_'+(seq.order_in_tuple+1).to_s)
trim_size=-1
if tr_size
trim_size=tr_size.to_i
end
# $WORKER_LOG.info "TRIM_SIZE=#{trim_size}, #{seq.order_in_tuple+1}"
if trim_size>0
if (seq.seq_fasta.size > trim_size)
a_beg,a_end = trim_size, seq.seq_fasta.size # position from an empty insert
actions=[]
type = "ActionTrim"
a=seq.new_action(a_beg,a_end,type)
actions.push a
add_stats('trim_sizes',a_end-a_beg+1)
seq.add_actions(actions)
end
end
end
#Returns an array with the errors due to parameters are missing
def self.check_params(params)
errors=[]
self.check_param(errors,params,'trim_size_file_1','Integer',-1)
self.check_param(errors,params,'trim_size_file_2','Integer',-1)
return errors
end
end
Version data entries
3 entries across 3 versions & 1 rubygems