Mercurial > repos > bcclaywell > argo_navis

annotate bin/parse_pact_tree.py @ 2:7eaf6f9abd28 draft default tip

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b-dirty
author bcclaywell
date Mon, 12 Oct 2015 17:57:38 -0400
parents d67268158946
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python
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2 import argparse
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3 import csv
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4 import re
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6
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7 coord_re = re.compile("\{([-\d\.]+),([-\d\.]+)\}")
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8
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9
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10 def parse_rules(handle):
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11 # Returns a very raw and literal translation of the out.rules results from PACT
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12 def get_nodes(line):
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13 return [int(x) for x in line.split()]
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14
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15 def int_if_intable(a):
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16 try:
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17 return int(a)
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18 except:
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19 return a
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20
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21 def get_map(line, imgfn=int_if_intable):
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22 coll = (x.split('->') for x in line.split())
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23 return dict([(int_if_intable(a), imgfn(b)) for a, b in coll])
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24
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25 def parse_coordinate(text):
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26 m = coord_re.match(text)
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27 return (float(m.group(1)), float(m.group(2)))
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28
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29 tips = get_nodes(handle.next())
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30 trunk_nodes = get_nodes(handle.next())
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31 connections = get_map(handle.next())
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32 labels = get_map(handle.next())
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33 coordinates = get_map(handle.next(), parse_coordinate)
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34 tip_names = get_map(handle.next(), str)
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35 return dict(tips=tips, trunk_nodes=trunk_nodes, connections=connections, labels=labels,
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36 coordinates=coordinates, tip_names=tip_names)
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37
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38
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39 def get_row(parsed_tree, n_id):
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40 # This gives us the row data (as seen in final table) for the given n_id value
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41 if n_id in parsed_tree['tips']:
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42 klass = "tip"
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43 name = parsed_tree['tip_names'][n_id]
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44 else:
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45 klass = "trunk"
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46 name = ""
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47 try:
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48 parent_id = parsed_tree['connections'][n_id]
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49 except KeyError:
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50 parent_id = n_id
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51 klass = "root"
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52 label = parsed_tree['labels'][n_id]
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53
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54 x, y = parsed_tree['coordinates'][n_id]
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55 parent_x, parent_y = parsed_tree['coordinates'][parent_id]
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56
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57 return dict(id=n_id, klass=klass, name=name, parent_id=parent_id, x=x, y=y, parent_x=parent_x,
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58 parent_y=parent_y, label=label)
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59
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60
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61 def parsed_to_table(parsed_tree):
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62 # Cols are going to be:
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63 # id, parent_id, label, klass, name, x, y, parent_x, parent_y,
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64 for n_id in parsed_tree['coordinates'].keys():
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65 yield get_row(parsed_tree, n_id)
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66
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67
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68 def get_args():
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69 parser = argparse.ArgumentParser(prog="parse_pact_tree.py",
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70 description="""Utility for parsing the output of PACT into a form renderable by ggplot""")
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71 parser.add_argument('input', type=argparse.FileType('r'))
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72 parser.add_argument('output', type=argparse.FileType('w'))
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73 return parser.parse_args()
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74
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75
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76 def main():
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77 # Get args, run the parser, spit out the results into a file
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78 args = get_args()
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79 data = parse_rules(args.input)
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80
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81 writer = csv.DictWriter(args.output,
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82 fieldnames=["id", "parent_id", "label", "klass", "name", "x", "y", "parent_x", "parent_y"])
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83 writer.writeheader()
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84
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85 for row in parsed_to_table(data):
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86 writer.writerow(row)
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87
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88 args.input.close()
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89 args.output.close()
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90
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91
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92 if __name__ == '__main__':
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93 main()
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94
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