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annotate scatterplot.py @ 3:1dacc8aeb452 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 93df3895fbf2fa44ff279303093fb89b79081687
author devteam
date Thu, 15 Sep 2016 05:36:51 -0400
parents 53eb2c412783
children 113045fca1aa
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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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6 from numpy import array
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7 import rpy2.rpy_classic as rpy
1dacc8aeb452 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 93df3895fbf2fa44ff279303093fb89b79081687
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8 from rpy2.robjects.numpy2ri import numpy2ri
1dacc8aeb452 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 93df3895fbf2fa44ff279303093fb89b79081687
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11 rpy.set_default_mode(rpy.NO_CONVERSION)
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12 r = rpy.r
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15 def stop_err(msg):
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16 sys.stderr.write(msg)
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17 sys.exit()
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18
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19
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20 def main():
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21
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22 in_fname = sys.argv[1]
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23 out_fname = sys.argv[2]
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24 try:
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25 columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
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26 except:
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27 stop_err( "Columns not specified, your query does not contain a column of numerical data." )
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28 title = sys.argv[5]
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29 xlab = sys.argv[6]
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30 ylab = sys.argv[7]
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31
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32 matrix = []
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33 skipped_lines = 0
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34 first_invalid_line = 0
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35 invalid_value = ''
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36 invalid_column = 0
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37 i = 0
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38 for i, line in enumerate( file( in_fname ) ):
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39 valid = True
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40 line = line.rstrip( '\r\n' )
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41 if line and not line.startswith( '#' ):
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42 row = []
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43 fields = line.split( "\t" )
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44 for column in columns:
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45 try:
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46 val = fields[column]
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47 if val.lower() == "na":
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48 row.append( float( "nan" ) )
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49 else:
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50 row.append( float( fields[column] ) )
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51 except:
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52 valid = False
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53 skipped_lines += 1
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54 if not first_invalid_line:
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55 first_invalid_line = i + 1
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56 try:
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57 invalid_value = fields[column]
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58 except:
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59 invalid_value = ''
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60 invalid_column = column + 1
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61 break
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62 else:
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63 valid = False
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64 skipped_lines += 1
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65 if not first_invalid_line:
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66 first_invalid_line = i + 1
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68 if valid:
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69 matrix.append( row )
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70
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71 if skipped_lines < i:
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72 try:
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73 a = numpy2ri(array( matrix ))
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74 r.pdf( out_fname, 8, 8 )
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75 r.plot( a, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
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76 r.dev_off()
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77 except Exception, exc:
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78 stop_err( "%s" % str( exc ) )
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79 else:
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80 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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81
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82 print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] )
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83 if skipped_lines > 0:
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84 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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85
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86 if __name__ == "__main__":
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87 main()