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annotate visualization.py @ 4:e520fbedf79b draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:38:20 +0000
parents a365150d73c0
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a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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1 #!/usr/bin/env python
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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2 """Visualise the output of Heinz.
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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4 This script is used to visualize the output of Heinz, which is in the form of
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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5 DOT language:
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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6 1. Clear the output of Heinz, extract the DOT source code.
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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7 2. Visualize the DOT source code and save it into file.
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9 The function of this script is rather simple, for more advanced visualization,
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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10 please adopt other solutions mentioned in the paper
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11 doi: 10.1093/bioinformatics/btv526
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12
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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13 This tool is only designed for visualizing the output of Heinz tool.
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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14 """
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a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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16 # Author: Cico Zhang
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17 # Date: 2 Aug 2017
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18 # Version: 0.2
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20 import argparse
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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21 import sys
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23 from graphviz import Source
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26 def get_args():
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27 """Collect the inputs."""
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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28 parser = argparse.ArgumentParser(
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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29 description='Visualise the output of Heinz')
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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30 parser.add_argument('-i', '--input', required=True, dest='heinz',
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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31 metavar='Heinz_output.txt', type=str,
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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32 help='Output file of Heinz as the input')
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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33 parser.add_argument('-o', '--output', required=True, dest='output',
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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34 metavar='graph.pdf', type=str,
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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35 help='The output file that saves the visualisation')
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36 args = parser.parse_args()
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37
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38 if args.heinz is None:
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39 sys.exit('Input file must be designated.')
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40
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41 return args
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44 def main():
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45 """Main function."""
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46 args = get_args()
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47 # Read the whole output file
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48 with open(args.heinz) as r:
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49 graph_dot = r.readlines()
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50
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51 # Remove the redundant lines
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52 while not graph_dot[0].startswith('graph G {'):
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53 graph_dot.pop(0)
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54
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55 src = Source(''.join(graph_dot))
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56 data_pdf = src.pipe('pdf')
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57 # Redirect the output (very important)
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58 with open(args.output, 'wb') as w:
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59 w.write(data_pdf)
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60 print('The visualization is saved as PDF!')
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61 sys.exit(0)
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62
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63
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64 if __name__ == "__main__":
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65 main()