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linesWithErrorBar.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#from __future__ import division, with_statement
'''
Copyright 2010, 陈同 (chentong_biology@163.com).
Please see the license file for legal information.
===========================================================
'''
__author__ = 'chentong & ct586[9]'
__author_email__ = 'chentong_biology@163.com'
#=========================================================
import sys
import os
def main():
if len(sys.argv) < 2 :
print >>sys.stderr, "Output an eps and pdf graph file with the \
filename given as prefix."
print >>sys.stderr, '''
File Format:(with a header line, startswith a '#'. This is necessary
and is used to annotate the first line not as data.)
#sample iso1 ylow yhigh iso2 ylow yhigh
sample1 0.345 0.1 0.55 0.35 0.43 0.89
sample2 1.234 1.0 1.3 9.23 20.1 0
sample3 5.02 5 6 3.42 0.33 0.01
sample4 5.60 5.5 6.2 0.01 0.03 4.3
#######################
Note: sample column is the x-axis label
sample row is the legend
The column number is not allowed to be larger than 37.
'''
print >>sys.stderr, 'Using python %s filename \
legend[default with legend, which is your itms in your first line, \
if there are many items, it would be better to tun it off by supply\
a 0 here.] xtics[default 1 means text xtics , if number supply a 0] \
preaditionallines[; seperate multiple lines] postaditionallines \
xlabel ylabel title [lines or linespoints]' % sys.argv[0]
sys.exit(0)
#---------------------------------
lenpara = len(sys.argv)
legendornot = 1
if lenpara >= 3:
legendornot = int(sys.argv[2])
#-------------------------------
xticsornot = 1 #text xtics
xticsvalue = ''
if lenpara >= 4:
xticsornot = int(sys.argv[3])
xticsvalue = '1:'
#-------------------------------
pregnu = ''
if lenpara >= 5:
pregnu = sys.argv[4]
#-------------------------------
postgnu = ''
if lenpara >= 6:
postgnu = sys.argv[5]
#-------------------------------
xlabel = ''
if lenpara >= 7:
xlabel = sys.argv[6]
#-------------------------------
ylabel = ''
if lenpara >= 8:
ylabel = sys.argv[7]
#-------------------------------
title = ''
if lenpara >= 9:
title = sys.argv[8]
#-------------------------------
style = 'lines'
if lenpara >=10:
style = sys.argv[9]
#-------------------------------
lsDict = {2:' ls 1', 3:' ls 2', 4:' ls 3', 5:' ls 4',
6:' ls 5', 7:' ls 6', 8:' ls 7', 9:' ls 8',
10:' ls 9', 11:' ls 10', 12:' ls 11', 13:' ls 12',
14:' ls 13', 15:' ls 14', 16:' ls 15', 17:' ls 16',
18:' ls 17', 19:' ls 18', 20:' ls 19', 21:' ls 20',
22:' ls 21', 23:' ls 22', 24:' ls 23', 25:' ls 24',
26:' ls 25', 27:' ls 26', 28:' ls 27', 29:' ls 28',
30:' ls 29', 31:' ls 30', 32:' ls 31', 33:' ls 32',
34:' ls 33', 35:' ls 34', 36:' ls 35', 37:' ls 36'
}
#-----------------------------
sample = []
header = 1
for line in open(sys.argv[1]):
if header:
header = 0
lineL = line.strip().split("\t")
plot = 'plot ' + '\'' + sys.argv[1] + '\' '
pos = 1
lenLineL = len(lineL)
for i in range(1, lenLineL, 3):
item = lineL[i]
pos += 1
errorbar = ':'.join((str(pos),str(pos+1),str(pos+2)))
if pos == 2:
plot += 'using ' + xticsvalue + str(pos) + \
' title ' + '\'' +\
item + '\'' + ' with ' + style + lsDict[pos]
plot += ',\'\' using ' + xticsvalue + errorbar + \
' with errorbar notitle' + lsDict[pos]
else:
plot += ',\'\' using ' + xticsvalue + str(pos) + ' title ' + '\'' +\
item + '\'' + ' with ' + style + lsDict[pos]
plot += ',\'\' using ' + xticsvalue + errorbar + \
' with errorbar notitle' + lsDict[pos]
#---------------------------------------
else:
tmp = line.split("\t",1)[0]
sample.append(tmp)
#--------------------------------------------
xtics = 'set xtics ('
i48 = -1
for item in sample:
i48 += 1
if item == '-':
continue
if i48 == 0:
xtics += '\'' + item + '\' ' + str(i48)
else:
xtics += ',\'' + item + '\' ' + str(i48)
xtics += ')'
#------------------------------
xrange='set xrange [-0.5:' + str(i48+0.5) + ']'
#------------------------------
fileout = sys.argv[1] + '.plt'
fh = open(fileout , 'w')
print >>fh, 'set term postscript eps color'
print >>fh, "set output \'" + sys.argv[1] + '.eps\''
print >>fh, '''
set style line 1 lt 1 linecolor rgb "red" lw 3
set style line 2 lt 1 linecolor rgb "orange" lw 3
set style line 3 lt 1 linecolor rgb "#000000" lw 3
set style line 4 lt 1 linecolor rgb "green" lw 3
set style line 5 lt 1 linecolor rgb "cyan" lw 3
set style line 6 lt 1 linecolor rgb "blue" lw 3
set style line 7 lt 1 linecolor rgb "violet" lw 3
set style line 8 lt 1 linecolor rgb "olive" lw 3
set style line 9 lt 1 linecolor rgb "purple" lw 3
set style line 10 lt 2 linecolor rgb "red" lw 3
set style line 11 lt 2 linecolor rgb "orange" lw 3
set style line 12 lt 2 linecolor rgb "#000000" lw 3
set style line 13 lt 2 linecolor rgb "green" lw 3
set style line 14 lt 2 linecolor rgb "cyan" lw 3
set style line 15 lt 2 linecolor rgb "blue" lw 3
set style line 16 lt 2 linecolor rgb "violet" lw 3
set style line 17 lt 2 linecolor rgb "olive" lw 3
set style line 18 lt 2 linecolor rgb "purple" lw 3
set style line 19 lt 3 linecolor rgb "red" lw 3
set style line 20 lt 3 linecolor rgb "orange" lw 3
set style line 21 lt 3 linecolor rgb "#000000" lw 3
set style line 22 lt 3 linecolor rgb "green" lw 3
set style line 23 lt 3 linecolor rgb "cyan" lw 3
set style line 24 lt 3 linecolor rgb "blue" lw 3
set style line 25 lt 3 linecolor rgb "violet" lw 3
set style line 26 lt 3 linecolor rgb "olive" lw 3
set style line 27 lt 3 linecolor rgb "purple" lw 3
set style line 28 lt 3 linecolor rgb "red" lw 3
set style line 29 lt 3 linecolor rgb "orange" lw 3
set style line 30 lt 3 linecolor rgb "#000000" lw 3
set style line 31 lt 3 linecolor rgb "green" lw 3
set style line 32 lt 3 linecolor rgb "cyan" lw 3
set style line 33 lt 3 linecolor rgb "blue" lw 3
set style line 34 lt 3 linecolor rgb "violet" lw 3
set style line 35 lt 3 linecolor rgb "olive" lw 3
set style line 36 lt 3 linecolor rgb "purple" lw 3
'''
if not legendornot:
print >>fh, "set nokey"
if xticsornot:
print >>fh, xrange
print >>fh, xtics
if pregnu:
print >>fh, pregnu
#----------------------------
if xlabel:
print >>fh, 'set xlabel \"%s\"' % xlabel
if ylabel:
print >>fh, 'set ylabel \"%s\"' % ylabel
if title:
print >>fh, 'set title \"%s\"' % title
#-----------------------------
print >>fh, plot
if postgnu:
print >>fh, postgnu
print >>fh, 'exit'
fh.close()
cmd1 = 'gnuplot ' + fileout
cmd2 = 'convert -density 300 -flatten ' + sys.argv[1] + '.eps ' +\
sys.argv[1] + '.png'
os.system(cmd1)
os.system(cmd2)
if __name__ == '__main__':
main()