Mercurial > repos > mvdbeek > scatterplot_test

annotate scatterplot.py @ 0:11627baf830e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
author mvdbeek
date Wed, 14 Sep 2016 12:40:20 -0400
parents
children b4102b163488
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0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
1 #!/usr/bin/env python
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
2 # Greg Von Kuster
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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3
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
4 import sys
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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5
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
6 from numpy import array
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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7 from rpy import r
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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8
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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9
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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10 def stop_err(msg):
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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11 sys.stderr.write(msg)
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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12 sys.exit()
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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13
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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14
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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15 def main():
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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16
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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17 in_fname = sys.argv[1]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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18 out_fname = sys.argv[2]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
19 try:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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20 columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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21 except:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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22 stop_err( "Columns not specified, your query does not contain a column of numerical data." )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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23 title = sys.argv[5]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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24 xlab = sys.argv[6]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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25 ylab = sys.argv[7]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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26
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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27 matrix = []
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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28 skipped_lines = 0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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29 first_invalid_line = 0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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30 invalid_value = ''
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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31 invalid_column = 0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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32 i = 0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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33 for i, line in enumerate( file( in_fname ) ):
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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34 valid = True
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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35 line = line.rstrip( '\r\n' )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
36 if line and not line.startswith( '#' ):
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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37 row = []
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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38 fields = line.split( "\t" )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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39 for column in columns:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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40 try:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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41 val = fields[column]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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42 if val.lower() == "na":
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
43 row.append( float( "nan" ) )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
44 else:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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45 row.append( float( fields[column] ) )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
46 except:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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47 valid = False
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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48 skipped_lines += 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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49 if not first_invalid_line:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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50 first_invalid_line = i + 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
51 try:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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52 invalid_value = fields[column]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
53 except:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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54 invalid_value = ''
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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55 invalid_column = column + 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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56 break
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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57 else:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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58 valid = False
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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59 skipped_lines += 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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60 if not first_invalid_line:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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61 first_invalid_line = i + 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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62
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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63 if valid:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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64 matrix.append( row )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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65
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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66 if skipped_lines < i:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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67 try:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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68 r.pdf( out_fname, 8, 8 )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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69 r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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70 r.dev_off()
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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71 except Exception, exc:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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72 stop_err( "%s" % str( exc ) )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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73 else:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
74 stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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75
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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76 print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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77 if skipped_lines > 0:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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78 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 )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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79
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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80 r.quit( save="no" )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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81
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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82 if __name__ == "__main__":
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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83 main()