Mercurial > repos > iuc > heinz
view visualization.py @ 3:2b80a2596064 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit 8007f71281553ddfa45e6f8e1172952d956bb000"
author | iuc |
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date | Thu, 11 Jun 2020 07:18:17 -0400 |
parents | e41ec5af7472 |
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#!/usr/bin/env python """Visualise the output of Heinz. This script is used to visualize the output of Heinz, which is in the form of DOT language: 1. Clear the output of Heinz, extract the DOT source code. 2. Visualize the DOT source code and save it into file. The function of this script is rather simple, for more advanced visualization, please adopt other solutions mentioned in the paper doi: 10.1093/bioinformatics/btv526 This tool is only designed for visualizing the output of Heinz tool. """ # Author: Cico Zhang # Date: 2 Aug 2017 # Version: 0.2 import argparse import sys from graphviz import Source def get_args(): """Collect the inputs.""" parser = argparse.ArgumentParser( description='Visualise the output of Heinz') parser.add_argument('-i', '--input', required=True, dest='heinz', metavar='Heinz_output.txt', type=str, help='Output file of Heinz as the input') parser.add_argument('-o', '--output', required=True, dest='output', metavar='graph.pdf', type=str, help='The output file that saves the visualisation') args = parser.parse_args() if args.heinz is None: sys.exit('Input file must be designated.') return args def main(): """Main function.""" args = get_args() # Read the whole output file with open(args.heinz) as r: graph_dot = r.readlines() # Remove the redundant lines while not graph_dot[0].startswith('graph G {'): graph_dot.pop(0) src = Source(''.join(graph_dot)) data_pdf = src.pipe('pdf') # Redirect the output (very important) with open(args.output, 'wb') as w: w.write(data_pdf) print('The visualization is saved as PDF!') sys.exit(0) if __name__ == "__main__": main()