--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bar_chart_plot.py	Tue Nov 27 14:20:40 2018 -0500
@@ -0,0 +1,140 @@
+#!/usr/bin/env python
+"""
+histogram_gnuplot.py <datafile> <xtic column> <column_list> <title> <ylabel> <yrange_min> <yrange_max> <grath_file>
+a generic histogram builder based on gnuplot backend
+
+   data_file    - tab delimited file with data
+   xtic_column  - column containing labels for x ticks [integer, 0 means no ticks]
+   column_list  - comma separated list of columns to plot
+   title        - title for the entire histrogram
+   ylabel       - y axis label
+   yrange_max   - minimal value at the y axis (integer)
+   yrange_max   - maximal value at the y_axis (integer)
+                  to set yrange to autoscaling assign 0 to yrange_min and yrange_max
+   graph_file   - file to write histogram image to
+   img_size     - as X,Y pair in pixels (e.g., 800,600 or 600,800 etc.)
+
+
+   This tool required gnuplot and gnuplot.py
+
+anton nekrutenko | anton@bx.psu.edu
+"""
+
+import string
+import sys
+import tempfile
+
+import Gnuplot
+import Gnuplot.funcutils
+
+assert sys.version_info[:2] >= (2, 4)
+
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+
+def main(tmpFileName):
+    skipped_lines_count = 0
+    skipped_lines_index = []
+    gf = open(tmpFileName, 'w')
+
+    try:
+        in_file = open(sys.argv[1], 'r')
+        xtic = int(sys.argv[2])
+        col_list = string.split(sys.argv[3], ",")
+        title = 'set title "' + sys.argv[4] + '"'
+        ylabel = 'set ylabel "' + sys.argv[5] + '"'
+        ymin = sys.argv[6]
+        ymax = sys.argv[7]
+        img_file = sys.argv[8]
+        img_size = sys.argv[9]
+    except:
+        stop_err("Check arguments\n")
+
+    try:
+        int(col_list[0])
+    except:
+        stop_err('You forgot to set columns for plotting\n')
+
+    for i, line in enumerate(in_file):
+        valid = True
+        line = line.rstrip('\r\n')
+        if line and not line.startswith('#'):
+            row = []
+            try:
+                fields = line.split('\t')
+                for col in col_list:
+                    row.append(str(float(fields[int(col) - 1])))
+            except:
+                valid = False
+                skipped_lines_count += 1
+                skipped_lines_index.append(i)
+        else:
+            valid = False
+            skipped_lines_count += 1
+            skipped_lines_index.append(i)
+
+        if valid and xtic > 0:
+            row.append(fields[xtic - 1])
+        elif valid and xtic == 0:
+            row.append(str(i))
+
+        if valid:
+            gf.write('\t'.join(row))
+            gf.write('\n')
+
+    if skipped_lines_count < i:
+        # Prepare 'using' clause of plot statement
+        g_plot_command = ' '
+
+        # Set the first column
+        if xtic > 0:
+            g_plot_command = "'%s' using 1:xticlabels(%s) ti 'Column %s', " % (tmpFileName, str(len(row)), col_list[0])
+        else:
+            g_plot_command = "'%s' using 1 ti 'Column %s', " % (tmpFileName, col_list[0])
+
+        # Set subsequent columns
+        for i in range(1, len(col_list)):
+            g_plot_command += "'%s' using %s t 'Column %s', " % (tmpFileName, str(i + 1), col_list[i])
+
+        g_plot_command = g_plot_command.rstrip(', ')
+
+        yrange = 'set yrange [' + ymin + ":" + ymax + ']'
+
+        try:
+            g = Gnuplot.Gnuplot()
+            g('reset')
+            g('set boxwidth 0.9 absolute')
+            g('set style fill  solid 1.00 border -1')
+            g('set style histogram clustered gap 5 title  offset character 0, 0, 0')
+            g('set xtics border in scale 1,0.5 nomirror rotate by 90 offset character 0, 0, 0')
+            g('set key invert reverse Left outside')
+            if xtic == 0:
+                g('unset xtics')
+            g(title)
+            g(ylabel)
+            g_term = 'set terminal png tiny size ' + img_size
+            g(g_term)
+            g_out = 'set output "' + img_file + '"'
+            if ymin != ymax:
+                g(yrange)
+            g(g_out)
+            g('set style data histograms')
+            g.plot(g_plot_command)
+        except:
+            stop_err("Gnuplot error: Data cannot be plotted")
+    else:
+        sys.stderr.write('Column(s) %s of your dataset do not contain valid numeric data' % sys.argv[3])
+
+    if skipped_lines_count > 0:
+        sys.stdout.write('\nWARNING. You dataset contain(s) %d invalid lines starting with line #%d.  These lines were skipped while building the graph.\n' % (skipped_lines_count, skipped_lines_index[0] + 1))
+
+
+if __name__ == "__main__":
+    # The tempfile initialization is here because while inside the main() it seems to create a condition
+    # when the file is removed before gnuplot has a chance of accessing it
+    gp_data_file = tempfile.NamedTemporaryFile('w')
+    Gnuplot.gp.GnuplotOpts.default_term = 'png'
+    main(gp_data_file.name)