Mercurial > repos > bcclaywell > argo_navis

annotate bin/pact_wrapper.py @ 0:d67268158946 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
1 #!/usr/bin/env python
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
2
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
3 import argparse
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
4 from os import path
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
5 import re
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
6 import os
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
7 import csv
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
8 import shutil
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
9 import subprocess
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
10
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
11
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
12 setting_template = """
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
13 # TREE MANIPULATION
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
14 {prune}
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
15
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
16 # TREE OUTPUT
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
17 print rule tree # print out the tree...
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
18
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
19 # SUMMARY STATS
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
20 summary tmrca # time to mrca
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
21 summary proportions # proportions on trunk of geneology
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
22 summary coal rates # coalescent rates; separate for each label
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
23 summary mig rates # migration rates; separate for each label pair
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
24 #summary fst # diversity between vs within labels
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
25
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
26 skyline settings -{sky_start} -{sky_end} {sky_interval}
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
27 skyline proportions
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
28 """
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
29
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
30
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
31 def tips_from_label(meta_reader, label, deme_col="deme"):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
32 return [row['sequence'] for row in meta_reader if row[deme_col] == label]
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
33
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
34 def tips_from_labels(meta_reader, labels, deme_col="deme"):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
35 return [row['sequence'] for row in meta_reader if row[deme_col] in labels]
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
36
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
37 def translate_tips(tips, translation):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
38 result = list()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
39 for tip in tips:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
40 try:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
41 result.append(translation[tip])
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
42 except KeyError:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
43 pass
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
44 return result
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
45
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
46
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
47 def translation_from_nexus(handle):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
48 """This reads the seqname -> id translation from the trees file. Should probably eventually move this out
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
49 and into a separate file so that we can use the results in plotting. Not now though..."""
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
50 in_trans = False
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
51 trans = dict()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
52 for line in handle:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
53 if re.search("Translate", line):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
54 # This is the demarkator for the translation section of the nexus file
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
55 in_trans = True
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
56 continue
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
57 if in_trans:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
58 if re.match(";", line):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
59 # If we hit this, we've reached the end of the translation region
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
60 break
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
61 else:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
62 # Otherwise we're still in the Translate region, so populate trans
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
63 index, name = line.strip().strip(',').split()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
64 trans[name] = index
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
65 return trans
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
66
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
67
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
68 def prune_tips_string(tips, args):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
69 if args.translate_trees:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
70 trans = translation_from_nexus(file(args.trees_in))
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
71 tips = translate_tips(tips, trans)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
72 return "prune to tips " + " ".join(tips)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
73
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
74
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
75 def prune_string(args):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
76 if args.labels:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
77 if args.metadata:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
78 labels = args.labels.replace("\"", "").replace("'", "").split()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
79 print "Pruning to labels:", labels
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
80 tips = tips_from_labels(csv.DictReader(args.metadata), labels, deme_col=args.deme_col)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
81 print "Tips for labels are:", tips
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
82 return prune_tips_string(tips, args)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
83 else:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
84 return "prune to label " + args.labels
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
85
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
86 elif args.tip_file or args.tips:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
87 if args.tip_file:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
88 tips = args.tip_file.read().split()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
89 else:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
90 tips = args.tips.replace("'", "").replace("\"", "").split()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
91 print "Tips specified are:", tips
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
92 return prune_tips_string(tips, args)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
93 else:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
94 return ""
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
95
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
96
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
97 def get_args():
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
98 parser = argparse.ArgumentParser()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
99 parser.add_argument('trees_in')
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
100 parser.add_argument('-t', '--tips', help="List of tips in quotes")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
101 parser.add_argument('-T', '--tip-file', help="File of tips sep by space", type=argparse.FileType('r'))
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
102 parser.add_argument('-r', '--translate-trees', action="store_true", default=False,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
103 help="""If flagged, the trees_in file will be used for translating tip names from indices to actual
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
104 tip names; this is necessary for BEAST runs only""")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
105 parser.add_argument('-m', '--metadata', type=argparse.FileType('r'),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
106 help="""Required for filtering by deme/label with the beast method""")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
107 parser.add_argument('-l', '--labels')
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
108 parser.add_argument('-s', '--sky-start', default=2.0, type=float,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
109 help="How far back to compute skyline statistics (should be a potive number)")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
110 parser.add_argument('-S', '--trim-start', type=float,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
111 help="""Trim the tree from 0 back to the specified time; overrides sky-start for skyline plots.
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
112 (should be a positive number)""")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
113 parser.add_argument('-e', '--trim-end', default=0.0, type=float,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
114 help="Most recent time to trim to in time interval; will also be used for sky (should be non-negative)")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
115 parser.add_argument('-o', '--out-dir')
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
116 parser.add_argument('-p', '--prune-to-trunk', action="store_true", default=False)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
117 parser.add_argument('-d', '--deme-col', default="deme", help="Deme column in metadata file")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
118 return parser.parse_args()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
119
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
120
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
121 def main():
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
122 args = get_args()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
123
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
124 # Create the param file in the proper directory
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
125 outfile = file(path.join(args.out_dir, 'in.param'), 'w')
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
126
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
127 prune = prune_string(args)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
128 if args.prune_to_trunk:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
129 prune += "\nprune to trunk"
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
130
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
131 if args.trim_start:
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
132 prune += "\ntrim ends -%s -%s" % (args.trim_start, args.trim_end)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
133
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
134 sky_start = args.trim_start if args.trim_start else args.sky_start
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
135 sky_end = args.trim_end
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
136 sky_interval = abs(sky_end - sky_start) / 100
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
137 outfile.write(setting_template.format(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
138 prune=prune,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
139 sky_end=sky_end,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
140 sky_start=sky_start,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
141 sky_interval=sky_interval))
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
142 outfile.close()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
143
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
144 # Copy the tree file over to the directory
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
145 shutil.copyfile(args.trees_in, path.join(args.out_dir, 'in.trees'))
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
146
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
147 # Actually run PACT
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
148 os.chdir(args.out_dir)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
149 subprocess.check_call(['pact'])
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
150
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
151
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
152 if __name__ == '__main__':
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
153 main()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
154
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
155