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1 #!/usr/bin/env python
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2 #Greg Von Kuster
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3
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4 import sys
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5 #from rpy import *
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6 import rpy2.robjects as robjects
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7 from rpy2.robjects.packages import importr
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8 r = robjects.r
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9 grdevices = importr('grDevices')
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10
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11 def stop_err(msg):
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12 sys.stderr.write(msg)
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13 sys.exit()
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14
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15 def main():
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16
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17 in_fname = sys.argv[1]
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18 out_fname = sys.argv[2]
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19 try:
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20 columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
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21 except:
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22 stop_err( "Columns not specified, your query does not contain a column of numerical data." )
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23 title = sys.argv[5]
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24 xlab = sys.argv[6]
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25 ylab = sys.argv[7]
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26
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27 matrix = []
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28 skipped_lines = 0
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29 first_invalid_line = 0
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30 invalid_value = ''
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31 invalid_column = 0
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32 i = 0
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33 for i, line in enumerate( file( in_fname ) ):
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34 valid = True
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35 line = line.rstrip( '\r\n' )
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36 if line and not line.startswith( '#' ):
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37 row = []
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38 fields = line.split( "\t" )
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39 for column in columns:
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40 try:
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41 val = fields[column]
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42 if val.lower() == "na":
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43 row.append( float( "nan" ) )
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44 else:
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45 row.append( float( fields[column] ) )
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46 except:
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47 valid = False
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48 skipped_lines += 1
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49 if not first_invalid_line:
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50 first_invalid_line = i + 1
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51 try:
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52 invalid_value = fields[column]
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53 except:
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54 invalid_value = ''
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55 invalid_column = column + 1
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56 break
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57 else:
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58 valid = False
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59 skipped_lines += 1
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60 if not first_invalid_line:
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61 first_invalid_line = i+1
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62
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63 if valid:
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64 #matrix.append( row )
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65 matrix += row
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66
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67 if skipped_lines < i:
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68 try:
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69 fv = robjects.FloatVector(matrix)
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70 m = r['matrix'](fv, ncol=len(columns),byrow=True)
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71 r.pdf( out_fname, 8, 8 )
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72 #r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
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73 r.plot( m, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
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74 #r.dev_off()
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75 grdevices.dev_off()
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76 except Exception, exc:
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77 stop_err( "%s" %str( exc ) )
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78 else:
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79 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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80
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81 print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] )
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82 if skipped_lines > 0:
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83 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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84
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85 #r.quit( save="no" )
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86
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87 if __name__ == "__main__":
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88 main()
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