refactoring of assemble_pairs

[biopieces.git] / bp_bin / analyze_seq

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
deleted file mode 120000 (symlink)
index ac17cf2fa4271400f3de43e8b3fc3a978af2d509..0000000000000000000000000000000000000000
--- a/bp_bin/analyze_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/analyze_seq
\ No newline at end of file

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..2c38a274beeb593394ec5d33663d4dec1129de23
--- /dev/null
+++ b/bp_bin/analyze_seq
@@ -0,0 +1,62 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Analyze sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'maasha/biopieces'
+require 'maasha/seq'
+
+casts = []
+
+options = Biopieces.options_parse(ARGV, casts)
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    if record[:SEQ]
+      seq  = Seq.new_bp(record)
+      comp = seq.composition
+
+      comp.each_pair do |key,val|
+        record["RES[#{key}]"] = val
+      end
+
+      record["SOFT_MASK%"] = seq.soft_mask
+      record["HARD_MASK%"] = (comp["N"].to_f / (seq.len - seq.indels).to_f * 100.0).round(2)
+      record["GC%"]        = ((comp["G"] + comp["C"]).to_f / (seq.len - seq.indels).to_f * 100.0).round(2)
+    end
+
+    output.puts record
+  end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__