removed debug message

[biopieces.git] / bp_bin / length_seq

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
deleted file mode 120000 (symlink)
index b3a16a722598c8067642e1d75bb3e3bbd7f56fa6..0000000000000000000000000000000000000000
--- a/bp_bin/length_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/length_seq
\ No newline at end of file

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..04384db3660c7762ccb1b99f9500d8a2e4bd3dc5
--- /dev/null
+++ b/bp_bin/length_seq
@@ -0,0 +1,49 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Determines the length of each sequence in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'maasha/biopieces'
+
+casts = []
+
+options = Biopieces.options_parse(ARGV, casts)
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    record[:SEQ_LEN] = record[:SEQ].length if record[:SEQ]
+    output.puts record
+  end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__