added plot_nucleotide_distribution biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1902 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/plot_nucleotide_distribution b/bp_bin/plot_nucleotide_distribution
new file mode 100755 (executable)
index 0000000..3970299
--- /dev/null
+++ b/bp_bin/plot_nucleotide_distribution
@@ -0,0 +1,150 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2012 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
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Plot the nucleotide distribution in percent of sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'gnuplot'
+require 'narray'
+require 'pp'
+
+VEC_MAX   = 10_000
+
+terminals = "dumb,x11,aqua,post,pdf,png,svg"
+title     = "Nucleotide Distribution"
+xlabel    = "Sequence position"
+ylabel    = "Nucleotide distribution (%)"
+
+casts = []
+casts << {:long=>'no_stream', :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil,    :allowed=>nil,       :disallowed=>nil}
+casts << {:long=>'data_out',  :short=>'o', :type=>'file',   :mandatory=>false, :default=>nil,    :allowed=>nil,       :disallowed=>nil}
+casts << {:long=>'terminal',  :short=>'t', :type=>'string', :mandatory=>false, :default=>'dumb', :allowed=>terminals, :disallowed=>nil}
+casts << {:long=>'title',     :short=>'T', :type=>'string', :mandatory=>false, :default=>title,  :allowed=>nil,       :disallowed=>nil}
+casts << {:long=>'xlabel',    :short=>'X', :type=>'string', :mandatory=>false, :default=>xlabel, :allowed=>nil,       :disallowed=>nil}
+casts << {:long=>'ylabel',    :short=>'Y', :type=>'string', :mandatory=>false, :default=>ylabel, :allowed=>nil,       :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+max_len = 0 
+
+vec_a   = NArray.int(VEC_MAX)
+vec_t   = NArray.int(VEC_MAX)
+vec_c   = NArray.int(VEC_MAX)
+vec_g   = NArray.int(VEC_MAX)
+vec_n   = NArray.int(VEC_MAX)
+vec_tot = NArray.float(VEC_MAX)
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    if record[:SEQ]
+      seq = record[:SEQ].upcase
+
+      raise BiopiecesError, "sequence too long: #{seq.length} > #{VEC_MAX}" if seq.length > VEC_MAX
+
+      vec_seq = NArray.to_na(seq, "byte")
+
+      vec_a[0 ... seq.length]   += vec_seq.eq('A'.ord)
+      vec_t[0 ... seq.length]   += vec_seq.eq('T'.ord)
+      vec_c[0 ... seq.length]   += vec_seq.eq('C'.ord)
+      vec_g[0 ... seq.length]   += vec_seq.eq('G'.ord)
+      vec_n[0 ... seq.length]   += vec_seq.eq('N'.ord)
+      vec_tot[0 ... seq.length] += 1
+
+      max_len = seq.length if seq.length > max_len
+    end
+
+    output.puts record unless options[:no_stream]
+  end
+end
+
+x = (1 .. max_len).to_a
+a = ((vec_a / vec_tot) * 100)[0 ... max_len].to_a
+t = ((vec_t / vec_tot) * 100)[0 ... max_len].to_a
+c = ((vec_c / vec_tot) * 100)[0 ... max_len].to_a
+g = ((vec_g / vec_tot) * 100)[0 ... max_len].to_a
+n = ((vec_n / vec_tot) * 100)[0 ... max_len].to_a
+
+a.unshift 0.0
+t.unshift 0.0
+c.unshift 0.0
+g.unshift 0.0
+n.unshift 0.0
+
+Gnuplot.open do |gp|
+  Gnuplot::Plot.new(gp) do |plot|
+    plot.terminal options[:terminal]
+    plot.title    options[:title]
+    plot.xlabel   options[:xlabel]
+    plot.ylabel   options[:ylabel]
+    plot.output   options[:data_out] if options[:data_out]
+    plot.ytics    "out"
+    plot.xtics    "out"
+    plot.yrange   "[0:100]"
+    plot.xrange   "[0:#{max_len}]"
+    plot.auto     "fix"
+    plot.offsets  "1"
+    plot.key      "outside right top vertical Left reverse enhanced autotitles columnhead nobox"
+    plot.key      "invert samplen 4 spacing 1 width 0 height 0"
+    plot.style    "fill solid 0.5 border"
+    plot.style    "histogram rowstacked"
+    plot.style    "data histograms"
+    plot.boxwidth "0.75 absolute"
+
+    plot.data << Gnuplot::DataSet.new(n) do |ds|
+      ds.using = "1"
+      ds.with  = "histogram lt rgb \"black\""
+      ds.title = "N"
+    end
+
+    plot.data << Gnuplot::DataSet.new(g) do |ds|
+      ds.using = "1"
+      ds.with  = "histogram lt rgb \"yellow\""
+      ds.title = "G"
+    end
+
+    plot.data << Gnuplot::DataSet.new(c) do |ds|
+      ds.using = "1"
+      ds.with  = "histogram lt rgb \"blue\""
+      ds.title = "C"
+    end
+
+    plot.data << Gnuplot::DataSet.new(t) do |ds|
+      ds.using = "1"
+      ds.with  = "histogram lt rgb \"green\""
+      ds.title = "T"
+    end
+
+    plot.data << Gnuplot::DataSet.new(a) do |ds|
+      ds.using = "1"
+      ds.with  = "histogram lt rgb \"red\""
+      ds.title = "A"
+    end
+  end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__