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[jalview.git]
/
forester
/
ruby
/
evoruby
/
lib
/
evo
/
tool
/
multi_sequence_extractor.rb
diff --git
a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
index
a868b6a
..
0c525ad
100644
(file)
--- a/
forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
+++ b/
forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
@@
-292,17
+292,16
@@
module Evoruby
per_species_counter = 0
end
puts " " + species_counter.to_s + ":" + current_species + " [" + my_readlink + "]"
per_species_counter = 0
end
puts " " + species_counter.to_s + ":" + current_species + " [" + my_readlink + "]"
- log << species_counter.to_s + ": " + current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
+ log << species_counter.to_s << ": " << current_species << " [" + my_readlink + "]" << Constants::LINE_DELIMITER
species_counter += 1
end
species_counter += 1
end
- puts " " + seq_name
- log << " " + seq_name + Constants::LINE_DELIMITER
+ log << " " << seq_name << Constants::LINE_DELIMITER
per_species_counter = per_species_counter + 1
seq = nil
indices = current_msa.find_by_name_start( seq_name, true )
if indices.size == 1
per_species_counter = per_species_counter + 1
seq = nil
indices = current_msa.find_by_name_start( seq_name, true )
if indices.size == 1
- seq = current_msa.get_sequence( indices[ 0 ] )
+ seq = current_msa.get_sequence( indices[ 0 ] )
elsif indices.size == 0
# Not found, try finding by partial match.
begin
elsif indices.size == 0
# Not found, try finding by partial match.
begin
@@
-521,8
+520,8
@@
module Evoruby
end
def print_counts( per_species_counter, log, ld )
end
def print_counts( per_species_counter, log, ld )
- puts " [sum: " + per_species_counter.to_s + "]"
- log << " [sum: " + per_species_counter.to_s + "]" + ld
+ puts " sum: " + per_species_counter.to_s
+ log << " sum: " + per_species_counter.to_s + ld
end
def read_fasta_file( input )
end
def read_fasta_file( input )
@@
-537,7
+536,7
@@
module Evoruby
rescue Exception => e
Util.fatal_error( PRG_NAME, "error: " + e.to_s )
end
rescue Exception => e
Util.fatal_error( PRG_NAME, "error: " + e.to_s )
end
- if @seqs <= 600000
+ if @seqs <= 400000
@file_to_msa[ input ] = msa
@seqs += msa.get_number_of_seqs
puts " total seqs in memory: " + @seqs.to_s
@file_to_msa[ input ] = msa
@seqs += msa.get_number_of_seqs
puts " total seqs in memory: " + @seqs.to_s