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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
b499c72
..
31f0272
100644
(file)
--- a/
forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
+++ b/
forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
@@
-25,10
+25,10
@@
module Evoruby
PRG_NAME = "mse"
PRG_VERSION = "1.02"
PRG_DESC = "extraction of sequences by name from multiple multi-sequence ('fasta') files"
PRG_NAME = "mse"
PRG_VERSION = "1.02"
PRG_DESC = "extraction of sequences by name from multiple multi-sequence ('fasta') files"
- PRG_DATE = "2012.07.20"
- COPYRIGHT = "2008-2012 Christian M Zmasek"
+ PRG_DATE = "130322"
+ COPYRIGHT = "2008-2013 Christian M Zmasek"
CONTACT = "phylosoft@gmail.com"
CONTACT = "phylosoft@gmail.com"
- WWW = "www.phylosoft.org"
+ WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
HELP_OPTION_1 = 'help'
HELP_OPTION_2 = 'h'
HELP_OPTION_1 = 'help'
HELP_OPTION_2 = 'h'
@@
-254,9
+254,9
@@
module Evoruby
Util.fatal_error( PRG_NAME, "unexpected format: " + line )
end
species = values[ 0 ]
Util.fatal_error( PRG_NAME, "unexpected format: " + line )
end
species = values[ 0 ]
- if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA" || species == "EIMTE"
- next
- end
+ #if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA" || species == "EIMTE"
+ # next
+ #end
seq_name = values[ 1 ]
domain_ranges = nil
if ( values.length > 3 )
seq_name = values[ 1 ]
domain_ranges = nil
if ( values.length > 3 )
@@
-314,7
+314,7
@@
module Evoruby
per_species_counter.to_i
per_species_counter.to_i
- ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER )
+ ids_map_writer.write( normalized_id + "\t" + seq.get_name + Constants::LINE_DELIMITER )
orig_name = nil
if seq != nil
orig_name = nil
if seq != nil