HI Vijayalakshmi,
You can take tools/plotting/plotter.py as an example :
See line 81 :
png_out = out_file + '.png' # force it to png
So in your case :
You can force it to pdf :
output_file = sys.argv[2] +".pdf"
I think this should work.
Saket
On 2 July 2013 23:37, vijayalakshmi <vs49(a)buffalo.edu> wrote:
Hi,
I am writing a python script that will take in two parameters (an input
file and an ouput file name) , plot a graph and output it to the filename
specified.
PYTHON SCRIPT
#!/usr/bin/python
import sys
import numpy as np
import matplotlib.pyplot as plt
input_file = sys.argv[1]
output_file = sys.argv[2]
mydata = np.loadtxt(input_file)
plt.figure(1)
plt.plot(mydata[:,0],mydata[:,1],label = "Feature");
plt.plot(mydata[:,0],mydata[:,2], label = "Variance");
plt.xlabel('Distance from feature(bp)');
plt.ylabel('Score');
plt.title(sys.argv[1]);
plt.legend(loc="best")
plt.savefig(output_file)
SAMPLE COMMAND :
<command interpreter="python"> plot.py $ref_filename $out_file1
</command>
<inputs>
<param name="ref_filename" type="data"
format="gen,txt,gtf,bed" label="Reference/Coordination file"
help="Choose
a reference file"/>
</inputs>
<outputs>
<data name="out_file1" format="pdf" />
</outputs>
When I run this, I am getting the following error.
File
"/panfs/panfs.ccr.buffalo.edu/projects/mjbuck/galaxy/CistromeAP/tools/ArchTex/plot.py",
line 22, in <module>
plt.savefig(output_file)
File "/data/apps/python/lib/python2.6/site-packages/matplotlib/pyplot.py",
line 345, in savefig
return fig.savefig(*args, **kwargs)
File "/data/apps/python/lib/python2.6/site-packages/matplotlib/figure.py",
line 990, in savefig
self.canvas.print_figure(*args, **kwargs)
File
"/data/apps/python/lib/python2.6/site-packages/matplotlib/backend_bases.py",
line 1399, in print_figure
'%s.' % (format, ', '.join(formats)))
ValueError: Format "dat" is not supported.
Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz.
I don't know how to make the script extract ".pdf" from the
".dat"
Thanks,
VJ.
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