Mercurial > repos > peterjc > venn_list

annotate venn_list.py @ 15:367a0403b7d2 draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
author peterjc
date Thu, 07 May 2015 05:43:50 -0400
parents
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15
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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1 #!/usr/bin/env python
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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2 """Plot up to 3-way Venn Diagram using R limma vennDiagram (via rpy)
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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3
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peterjc
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4 This script is copyright 2010 by Peter Cock, The James Hutton Institute
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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5 (formerly SCRI), UK. All rights reserved.
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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6 See accompanying text file for licence details (MIT/BSD style).
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7
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peterjc
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8 This is version 0.0.8 of the script.
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peterjc
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9 """
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10
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11
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peterjc
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12 import sys
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
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13
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14 def sys_exit(msg, error_level=1):
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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15 """Print error message to stdout and quit with given error level."""
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peterjc
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16 sys.stderr.write("%s\n" % msg)
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17 sys.exit(error_level)
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18
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19 try:
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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20 import rpy
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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21 except ImportError:
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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22 sys_exit("Requires the Python library rpy (to call R)")
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peterjc
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23 except RuntimeError, e:
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24 sys_exit("The Python library rpy is not availble for the current R version\n\n%s" % e)
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25
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26 try:
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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27 rpy.r.library("limma")
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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28 except:
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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29 sys_exit("Requires the R library limma (for vennDiagram function)")
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30
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31
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32 if len(sys.argv)-1 not in [7, 10, 13]:
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
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33 sys_exit("Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" % (len(sys.argv)-1))
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34
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35 all_file, all_type, all_label = sys.argv[1:4]
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
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36 set_data = []
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37 if len(sys.argv)-1 >= 7:
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38 set_data.append(tuple(sys.argv[4:7]))
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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39 if len(sys.argv)-1 >= 10:
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
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40 set_data.append(tuple(sys.argv[7:10]))
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peterjc
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41 if len(sys.argv)-1 >= 13:
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peterjc
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42 set_data.append(tuple(sys.argv[10:13]))
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peterjc
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43 pdf_file = sys.argv[-1]
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peterjc
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44 n = len(set_data)
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
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45 print "Doing %i-way Venn Diagram" % n
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46
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47 def load_ids(filename, filetype):
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48 if filetype=="tabular":
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49 for line in open(filename):
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50 line = line.rstrip("\n")
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
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51 if line and not line.startswith("#"):
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52 yield line.split("\t",1)[0]
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peterjc
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53 elif filetype=="fasta":
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54 for line in open(filename):
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55 if line.startswith(">"):
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peterjc
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56 yield line[1:].rstrip("\n").split(None,1)[0]
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peterjc
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57 elif filetype.startswith("fastq"):
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58 #Use the Galaxy library not Biopython to cope with CS
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59 from galaxy_utils.sequence.fastq import fastqReader
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60 handle = open(filename, "rU")
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peterjc
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61 for record in fastqReader(handle):
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62 #The [1:] is because the fastaReader leaves the @ on the identifer.
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63 yield record.identifier.split()[0][1:]
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peterjc
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64 handle.close()
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65 elif filetype=="sff":
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66 try:
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67 from Bio.SeqIO import index
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68 except ImportError:
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69 sys_exit("Require Biopython 1.54 or later (to read SFF files)")
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70 #This will read the SFF index block if present (very fast)
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71 for name in index(filename, "sff"):
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72 yield name
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73 else:
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74 sys_exit("Unexpected file type %s" % filetype)
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75
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76 def load_ids_whitelist(filename, filetype, whitelist):
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77 for name in load_ids(filename, filetype):
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78 if name in whitelist:
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79 yield name
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80 else:
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peterjc
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81 sys_exit("Unexpected ID %s in %s file %s" % (name, filetype, filename))
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82
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83 if all_file in ["", "-", '""', '"-"']:
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peterjc
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84 #Load without white list
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peterjc
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85 sets = [set(load_ids(f,t)) for (f,t,c) in set_data]
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
peterjc
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86 #Take union
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87 all = set()
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peterjc
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88 for s in sets:
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89 all.update(s)
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90 print "Inferred total of %i IDs" % len(all)
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91 else:
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92 all = set(load_ids(all_file, all_type))
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93 print "Total of %i IDs" % len(all)
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94 sets = [set(load_ids_whitelist(f,t,all)) for (f,t,c) in set_data]
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95
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96 for s, (f,t,c) in zip(sets, set_data):
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97 print "%i in %s" % (len(s), c)
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98
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99 #Now call R library to draw simple Venn diagram
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peterjc
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100 try:
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
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101 #Create dummy Venn diagram counts object for three groups
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
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102 cols = 'c("%s")' % '","'.join("Set%i" % (i+1) for i in range(n))
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103 rpy.r('groups <- cbind(%s)' % ','.join(['1']*n))
367a0403b7d2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
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104 rpy.r('colnames(groups) <- %s' % cols)
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105 rpy.r('vc <- vennCounts(groups)')
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106 #Populate the 2^n classes with real counts
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107 #Don't make any assumptions about the class order
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peterjc
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108 #print rpy.r('vc')
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109 for index, row in enumerate(rpy.r('vc[,%s]' % cols)):
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peterjc
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110 if isinstance(row, int) or isinstance(row, float):
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peterjc
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111 #Hack for rpy being too clever for single element row
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112 row = [row]
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113 names = all
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peterjc
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114 for wanted, s in zip(row, sets):
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peterjc
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115 if wanted:
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116 names = names.intersection(s)
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117 else:
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118 names = names.difference(s)
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peterjc
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119 rpy.r('vc[%i,"Counts"] <- %i' % (index+1, len(names)))
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peterjc
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120 #print rpy.r('vc')
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121 if n == 1:
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peterjc
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122 #Single circle, don't need to add (Total XXX) line
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peterjc
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123 names = [c for (t,f,c) in set_data]
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peterjc
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124 else:
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peterjc
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125 names = ["%s\n(Total %i)" % (c, len(s)) for s, (f,t,c) in zip(sets, set_data)]
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peterjc
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126 rpy.r.assign("names", names)
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127 rpy.r.assign("colors", ["red","green","blue"][:n])
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128 rpy.r.pdf(pdf_file, 8, 8)
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129 rpy.r("""vennDiagram(vc, include="both", names=names,
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130 main="%s", sub="(Total %i)",
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131 circle.col=colors)
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132 """ % (all_label, len(all)))
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133 rpy.r.dev_off()
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peterjc
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134 except Exception, exc:
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135 sys_exit( "%s" %str( exc ) )
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136 rpy.r.quit( save="no" )
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137 print "Done"