added python based tsvplot

bin/tsvplot

@@ -1 +1 @@
-../tsv/tsvplot
+../tsv/tsvplot.py

tsv/tsvplot

@@ -1,33 +1,52 @@
 #!/bin/bash
 
-[[ -z "$3" ]] && {
+_helpexit() {
+  self=$( basename $0 )
   echo "Plot2D for console.
   
   Arguments
-  tsvplot  FILE xCol yCol [plotStyle] [preBlock]
+  $self  FILE xCol yCol [-X] [plotStyle] [preBlock]
   
-  e.g.  tsvplot cal.tsv 2 4 
+  e.g.  $self cal.tsv 2 4 
-  or    tsvplot cal.tsv Area Weight \"with lines;\" \"set title 'test plot';\" 
+  or    $self cal.tsv Area Weight \"with lines;\" \"set title 'test plot';\" 
   preBlock may contain any GNUPlot commands.
   plotStyle contains any plotting style commands.
   
+  -X    use X11 instead of console
   Requires  csvkit and gnuplot
   "
   exit
 }
 
-fbase=$( basename "$1" )
+if [ $# -lt 3 ]; then _helpexit; fi
 
-csvcut -t -c "$2,$3" "$1" | gnuplot -e "
+POS=0
-set term dumb $(tput cols) $(tput lines) enhanced; 
+POSADJUST=0
+for (( i=1; i<=$#; i++ )); do 
+  POS=$(( $i + $POSADJUST ))
+  [[ ${!i} = "-h" ]] && _helpexit
+  [[ ${!i} = "help" ]] && _helpexit
+  [[ ${!i} = "-X" ]] && PLOTTERM="  " && POSADJUST=$(( $POSADJUST - 1 )) && continue
+  [[ $POS -eq 1 ]] && FILE="${!i}"
+  [[ $POS -eq 2 ]] && XCOL="${!i}"
+  [[ $POS -eq 3 ]] && YCOL="${!i}"
+  [[ $POS -eq 4 ]] && STYLE="${!i}"
+  [[ $POS -eq 5 ]] && PRE="${!i}"
+done
+fbase=$( basename "$FILE" )
+[[ -z "$PLOTTERM" ]] && PLOTTERM="set term dumb $(tput cols) $(tput lines) enhanced;" 
+[[ -z "$PRE" ]]      && PRE="set title '$fbase';"
+
+csvcut -t -c "$XCOL,$YCOL" "$FILE" | gnuplot -p -e "$PLOTTERM
 set datafile separator \",\"; 
-set xlabel '$2'; 
+set xlabel '$XCOL'; 
-$5
+set ylabel '$YCOL'; 
-plot '<cat' using 1:2 title '$fbase $3' $4" 
+$PRE
+plot '<cat' using 1:2 title '' $STYLE" 
 
 [[ $? -ne 0 ]] && {
     echo -n "Possible columns: "
-    head -n 1 "$1" | tr \\t ,
+    head -n 1 "$FILE" | tr \\t ,
 } || {
     true
 }

tsv/tsvplot.py

@@ -0,0 +1,224 @@
+#!/usr/bin/env python
+#
+# Copyright 2016 Ville Rantanen
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as published
+# by the Free Software Foundation, either version 3 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 Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+from __future__ import print_function
+import sys, os, math, csv, subprocess
+from argparse import ArgumentParser 
+
+'''Plot CSV files with GNUPLOT.'''
+__author__ = "Ville Rantanen"
+__version__ = "0.1"
+
+def get_data_scatter(opts):
+    reader=csv.DictReader(open(os.path.join(*opts.csv),'rb'), dialect=csv.excel_tab, lineterminator="\n")
+    data=[]
+    try:
+        for row in reader:
+            data.append(",".join([row[c] for c in opts.columns]))
+    except KeyError,ME:
+        print("Column {} not found.".format(ME),file=sys.stderr)
+        print("Columns in the file:"+",".join(reader.fieldnames),file=sys.stderr)
+        sys.exit(1)
+    return "\n".join(data)
+
+def get_data_histogram(opts):
+    reader=csv.DictReader(open(os.path.join(*opts.csv),'rb'), dialect=csv.excel_tab, lineterminator="\n")
+    data=[]
+    try:
+        for row in reader:
+            try:
+                f=float(row[opts.columns[0]])
+                data.append(row[opts.columns[0]])
+            except ValueError:
+                continue
+    except KeyError,ME:
+        print("Column {} not found.".format(ME),file=sys.stderr)
+        print("Columns in the file:"+",".join(reader.fieldnames),file=sys.stderr)
+        sys.exit(1)
+    return "\n".join(data)
+    
+def get_stats(opts):
+    reader=csv.DictReader(open(os.path.join(*opts.csv),'rb'), dialect=csv.excel_tab, lineterminator="\n")
+    values_min=float('nan')
+    values_max=-float('nan')
+    values_n=0
+    try:
+        for row in reader:
+            try:
+                f=float(row[opts.columns[0]])
+            except ValueError:
+                continue
+            values_n+=1
+            values_min=min(f,values_min)
+            values_max=max(f,values_max)
+    except KeyError,ME:
+        print("Column {} not found.".format(ME),file=sys.stderr)
+        print("Columns in the file:"+",".join(reader.fieldnames),file=sys.stderr)
+        sys.exit(1)
+    return (values_min,values_max,values_n)
+   
+def get_plotterm(opts):   
+    if opts.X11:
+        plotterm=""
+    else:
+        (height,width)=termsize()
+        if opts.height:
+            height=opts.height
+        if opts.width:
+            width=opts.width
+        height+=2
+        plotterm="set term dumb {0} {1} enhanced;".format(width,height)
+    return plotterm
+
+def get_histogram_template(opts):
+    plotterm=get_plotterm(opts)
+    (vmin,vmax,vnum)=get_stats(opts)
+    if opts.bins:
+        bins=opts.bins
+    else:
+        bins=math.ceil(math.sqrt(vnum))
+        if not opts.X11:
+            (height,width)=termsize()
+            if opts.width:
+                width=opts.width
+            bins=min(int(float(width)/4),bins)
+    template='''{}
+set datafile separator ","; 
+set xlabel '{}';
+Min = {};
+Max = {};
+n = {:f};
+width = (Max-Min)/n;
+set boxwidth width absolute;
+bin(x) = width*(floor((x-Min)/width)+0.5) + Min;
+{}
+plot '<cat' u (bin($1)):(1.0) smooth freq title '' {};
+    '''.format(
+        plotterm,
+        opts.columns[0],
+        vmin,vmax,bins,
+        opts.pre,
+        opts.style
+    )
+    return template
+
+def get_scatterplot_template(opts):
+    plotterm=get_plotterm(opts)
+    template = '''{}
+set datafile separator ","; 
+set xlabel '{}'; 
+set ylabel '{}';
+{}
+plot '<cat' using 1:2 title '' {};'''.format(
+        plotterm,
+        opts.columns[0],
+        opts.columns[1],
+        opts.pre,
+        opts.style
+    )
+    return template
+    
+def run_gnuplot(opts, template, get_data):
+    p = subprocess.Popen(['gnuplot','-p','-e',template], stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE)
+    comm=p.communicate(input=get_data(opts))
+    for l in comm[0].split("\n"):
+        if not l.strip()=="":
+            print(l)
+    if p.returncode>0:
+        print(template)
+        print('='*25)
+        print(comm[1])
+    return(p.returncode)
+
+def which(program):
+    import os
+    def is_exe(fpath):
+        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+    fpath, fname = os.path.split(program)
+    if fpath:
+        if is_exe(program):
+            return program
+    else:
+        for path in os.environ["PATH"].split(os.pathsep):
+            exe_file = os.path.join(path, program)
+            if is_exe(exe_file):
+                return exe_file
+
+    return None
+
+def setup_options():
+    ''' Setup the command line options '''
+    
+    parser=ArgumentParser(description="Plot CSV columns to 2D scatter plot, or a histogram. Uses GNUPLOT command line utility to draw plots.")
+    parser.add_argument("-v","--version",action='version', version=__version__)
+    parser.add_argument("-c",action="store",dest="columns",type=str,required=True,
+                      help="Column name for histogram, or comma separated list of two names for scatter plot. First column is the x-axis.")
+    parser.add_argument("-d",action="store",dest="delimiter",default="\t",
+                      help="File delimiter, default [tab].")
+    parser.add_argument("-n",action="store",type=int,dest="bins",default=False,
+                      help="Bins for histograms. Default: min( console_width/4,sqrt(len(values)) )")
+    parser.add_argument("-p",action="store",dest="pre",default="",
+                      help="Gnuplot commands to execute before plotting.")
+    parser.add_argument("-s",action="store",dest="style",default=None,
+                      help="Plotting style, e.g. 'with lines'. Defaults to points for 2D plot, boxes for histogram.")    
+    parser.add_argument("--width",action="store",type=int,dest="width",default=False,
+                      help="Console width. Default: fullscreen")
+    parser.add_argument("--height",action="store",type=int,dest="height",default=False,
+                      help="Console height. Default: fullscreen")
+    parser.add_argument("-X",action="store_true",dest="X11",default=False,
+                      help="Show plot in X11 window, instead of console.")
+    parser.add_argument("-D",action="store_true",dest="debug",default=False,
+                      help="Print commands before execution")
+    
+    parser.add_argument("csv",type=str,action="store",
+                      help="CSV file to plot")
+    options=parser.parse_args()
+    options.columns=[c.strip() for c in options.columns.split(",")]
+    if len(options.columns)>2:
+        parser.error("Only two columns supported.")
+    options.csv=os.path.split(options.csv)
+    if not options.style:
+        if len(options.columns)==1:
+            options.style="with boxes;"
+        else:
+            options.style="pt '*'"
+    return options                
+
+def termsize():
+    try:
+        rows, columns = os.popen('stty size', 'r').read().split()
+    except:
+        (rows,columns)=(25,80)
+    return (int(rows),int(columns))
+    
+if not which('gnuplot'):
+    print('You don\'t seem to have "gnuplot" installed!')
+    sys.exit(1)
+
+opts=setup_options()
+
+if len(opts.columns)==1:
+    template=get_histogram_template(opts)
+    get_data=get_data_histogram
+else:
+    template=get_scatterplot_template(opts)
+    get_data=get_data_scatter
+if opts.debug:
+    print(template)
+rc=run_gnuplot(opts, template, get_data)
+sys.exit(rc)

tsv/tsvsummary

@@ -45,7 +45,7 @@ then usage
      exit 1
 fi
 
-which ncsv &> /dev/null || ( echo ncsv required: "https://code.google.com/p/nicecsv/"; exit 1 )
+which ncsv &> /dev/null || ( echo ncsv required: "https://bitbucket.org/MoonQ/ncsv"; exit 1 )
 which csvcut &> /dev/null || ( echo csvkit required: "https://csvkit.readthedocs.org/"; exit 1 )
 
 if [ -z "$LABEL" ]