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1 #!/usr/bin/env python
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2
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3 #-----------------------------------------------------------------------------
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4 # NAME: circlader.py
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5 # DESCRIPTION: Circlader (circular cladogram buider) is a python script for
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6 # creating images of circular cladogram starting from any guide
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7 # tree in tabular or Newick format
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8 #
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9 # Author: Nicola Segata
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10 # email: nsegata@hsph.harvard.edu
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11 #
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12 # Copyright: (c) 2011
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13 # Licence: <your licence>
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14 #
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15 #-----------------------------------------------------------------------------
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16
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17
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18 import os
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19 import sys,argparse
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20 import circlader_lib as cir
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21
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22 def read_params(args):
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23 parser = argparse.ArgumentParser(description='Circlader')
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24
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25 parser.add_argument('tree_file', nargs='?', default=None, type=str,
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26 help= "the input tree in Newick format (unless --tf is specified)"
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27 "[stdin if not present]")
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28 parser.add_argument('out_image', nargs='?', default=None, type=str,
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29 help= "the output image (the format is guessed from the extension "
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30 "[windows visualization if not present]")
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31 parser.add_argument('--tree_format', choices=['newick','tabular'],
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32 default='newick', type=str,
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33 help= "specifies the input tree format (default \"newick\", "
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34 "other choice is \"tabular\")")
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35 parser.add_argument('--style_file', nargs='?', default=os.getcwd()+"/default_styles/style.txt", type=str,
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36 help= "set the style file (default_styles/style.txt if not specified)")
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37 parser.add_argument('--color_file', nargs='?', default=None, type=str,
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38 help= "set the color file (default_styles/colors.txt if not specified)")
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39 parser.add_argument('--highlight_file', nargs='?', default=None, type=str,
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40 help= "set the highlight file (default none)")
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41 parser.add_argument('--tick_file', nargs='?', default=None, type=str,
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42 help= "set the label file for level's names (default none)")
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43 parser.add_argument('--size_file', nargs='?', default=None, type=str,
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44 help= "set the file containing the dimentison of the circles (default none)")
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45 parser.add_argument('--circle_file', nargs='?', default=None, type=str,
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46 help= "set the external circles file (default none) [BETA FEATURE]")
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47 parser.add_argument('--format', choices=['png','pdf','ps','eps','svg'], default=None, type=str,
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48 help= "set the format of the output image (default none "
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49 "meaning that the format is guessed from the output "
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50 "file extension)")
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51 parser.add_argument('--dpi', default=300, type=int )
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52
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53 return vars(parser.parse_args())
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54
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55 params = read_params(sys.argv)
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56
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57 cladogram = cir.Tree()
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58 cladogram.read_colors(params['color_file'])
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59 cladogram.read_style(params['style_file'])
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60 cladogram.read_sizes(params['size_file'])
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61 cladogram.read_circles(params['circle_file'])
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62 cladogram.read_highlights(params['highlight_file'])
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63 cladogram.read_tick_labels(params['tick_file'])
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64 if params['tree_format'] == 'newick':
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65 cladogram.load_newick(params['tree_file'])
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66 else:
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67 cladogram.load_lefse(params['tree_file'])
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68 cladogram.pos_rad_leaves()
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69 cladogram.set_pos()
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70 cladogram.draw(params['out_image'],outformat=params['format'],dpi=params['dpi'])
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