Mercurial > repos > crs4 > seal_galaxy

comparison seal-galaxy-cc1b1911/seal/recab_table_galaxy.py @ 0:244073d9abc1 draft default tip

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author crs4
date Wed, 15 Oct 2014 09:41:10 -0400
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1 #!/usr/bin/env python
2
3 # Copyright (C) 2011-2014 CRS4.
4 #
5 # This file is part of Seal.
6 #
7 # Seal is free software: you can redistribute it and/or modify it
8 # under the terms of the GNU General Public License as published by the Free
9 # Software Foundation, either version 3 of the License, or (at your option)
10 # any later version.
11 #
12 # Seal is distributed in the hope that it will be useful, but
13 # WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
14 # or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
15 # for more details.
16 #
17 # You should have received a copy of the GNU General Public License along
18 # with Seal. If not, see <http://www.gnu.org/licenses/>.
19
20
21
22 """
23 Calls the Seal RecabTable tool. Then, it calls recab_table_fetch to
24 concatenate all the partial tables and create a single csv file.
25 """
26
27
28 # parameters:
29 # INPUT_DATA
30 # OUTPUT
31 # VCF
32 # NUM_REDUCERS
33 # [OTHER]
34
35 import os
36 import sys
37
38 import hadoop_galaxy.pathset as pathset
39 import subprocess
40 import tempfile
41 import pydoop.hdfs as phdfs
42
43 # XXX: add --append-python-path to the possible arguments?
44
45 def usage_error(msg=None):
46 if msg:
47 print >> sys.stderr, msg
48 print >> sys.stderr, os.path.basename(sys.argv[0]), "INPUT_DATA OUTPUT VCF NUM_REDUCERS [OTHER]"
49 sys.exit(1)
50
51
52 def run_recab(input_path, output_path, vcf, num_red, other_args):
53 mydir = os.path.abspath(os.path.dirname(__file__))
54 cmd = [
55 'hadoop_galaxy',
56 '--input', input_path,
57 '--output', output_path,
58 '--executable', 'seal',
59 'recab_table',
60 '--vcf-file', vcf,
61 '--num-reducers', num_red
62 ]
63
64 if other_args:
65 cmd.extend(other_args)
66
67 # now execute the hadoop job
68 subprocess.check_call(cmd)
69
70 def collect_table(pset, output_path):
71 # finally, fetch the result into the final output file
72 cmd = ['seal', 'recab_table_fetch']
73 cmd.extend(pset.get_paths())
74 cmd.append(output_path)
75 try:
76 # remove the file that galaxy creates. recab_table_fetch refuses to
77 # overwrite it
78 os.unlink(output_path)
79 except IOError:
80 pass
81 subprocess.check_call(cmd)
82
83 def cleanup(out_pathset):
84 # clean-up job output
85 for path in out_pathset:
86 try:
87 print >> sys.stderr, "Deleting output path", path
88 phdfs.rmr(path)
89 except StandardError as e:
90 print >> sys.stderr, "Error!", str(e)
91
92 def main(args):
93 if len(args) < 5:
94 usage_error()
95
96 input_data = args[0]
97 final_output = args[1]
98 vcf = args[2]
99 num_reducers = args[3]
100 other = args[4:]
101
102 # Create a temporary pathset to reference the recab_table
103 # output directory
104 with tempfile.NamedTemporaryFile(mode='rwb') as tmp_pathset_file:
105 try:
106 run_recab(input_data, tmp_pathset_file.name, vcf, num_reducers, other)
107 tmp_pathset_file.seek(0)
108 out_paths = pathset.FilePathset.from_file(tmp_pathset_file)
109 collect_table(out_paths, final_output)
110 finally:
111 cleanup(out_paths)
112
113 if __name__ == "__main__":
114 main(sys.argv[1:])
115
116 # vim: et ai ts=2 sw=2