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 <v...@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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