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95 lines
2.9 KiB
Python
95 lines
2.9 KiB
Python
#!/usr/bin/env python
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#Greg Von Kuster
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import sys
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from rpy import *
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def stop_err(msg):
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sys.stderr.write(msg)
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sys.exit()
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def main():
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in_fname = sys.argv[1]
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out_fname = sys.argv[2]
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try:
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columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
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except:
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stop_err( "Columns not specified, your query does not contain a column of numerical data." )
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title = sys.argv[5]
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xlab = sys.argv[6]
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ylab = sys.argv[7]
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out_type = sys.argv[8]
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out_width = int(sys.argv[9])
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out_height = int(sys.argv[10])
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point_size = float(sys.argv[11])
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xvec=[]
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yvec=[]
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skipped_lines = 0
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first_invalid_line = 0
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invalid_value = ''
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invalid_column = 0
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i = 0
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for i, line in enumerate( file( in_fname ) ):
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valid = True
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vals = []
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line = line.rstrip( '\r\n' )
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if line and not line.startswith( '#' ):
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row = []
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fields = line.split( "\t" )
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for c,column in enumerate(columns):
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try:
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val = fields[column]
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if val.lower() == "na":
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v = float( "nan" )
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else:
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v = float( fields[column] )
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vals.append(val)
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except:
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valid = False
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = i + 1
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try:
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invalid_value = fields[column]
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except:
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invalid_value = ''
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invalid_column = column + 1
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break
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else:
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valid = False
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = i+1
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if valid:
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xvec.append(vals[0])
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yvec.append(vals[1])
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if skipped_lines < i:
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try:
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if out_type == "jpg":
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r.jpeg(out_fname,width=out_width,height=out_height)
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elif out_type == "png":
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# type="cairo" needed to be set for headless servers
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r.png(out_fname,type="cairo",width=out_width,height=out_height)
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else:
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r.pdf(out_fname, out_width, out_height)
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r.plot(xvec,yvec, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19,cex=point_size )
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r.dev_off()
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except Exception, exc:
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stop_err( "%s" %str( exc ) )
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else:
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stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) )
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print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] )
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if skipped_lines > 0:
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print "Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column )
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r.quit( save="no" )
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if __name__ == "__main__":
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main()
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