Mercurial > repos > galaxyp > peptideshaker
comparison reverse.py @ 2:fb591fc7241c draft
Improved some datatype handling
author | galaxyp |
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date | Thu, 20 Jun 2013 11:02:36 -0400 |
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1:7a74818e0eeb | 2:fb591fc7241c |
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1 from os.path import dirname, join, abspath | |
2 import sys | |
3 from optparse import OptionParser | |
4 from ConfigParser import SafeConfigParser | |
5 import subprocess | |
6 | |
7 DEBUG = False | |
8 | |
9 | |
10 def main(): | |
11 (options, args) = _parse_args() | |
12 format_args = (options.input, options.output) | |
13 _run_shell("cat '%s' > '%s'" % format_args) | |
14 _run_dbtoolkit("com.compomics.dbtoolkit.toolkit.ReverseFASTADB", "'%s' | head --lines -4 >> '%s'" % \ | |
15 format_args) | |
16 | |
17 | |
18 def _run_shell(command): | |
19 if DEBUG: | |
20 print "Running shell command %s" % command | |
21 _exec(command) | |
22 | |
23 | |
24 def _run_dbtoolkit(java_class, args): | |
25 command_prefix = "java -cp %s" % _dbtoolkit_jar_path() | |
26 _exec("%s %s %s" % (command_prefix, java_class, args)) | |
27 | |
28 | |
29 def _dbtoolkit_jar_path(): | |
30 py_path = __file__ | |
31 jar_path = join(dirname(py_path), "dbtoolkit-4.2", "dbtoolkit-4.2.jar") | |
32 return jar_path | |
33 | |
34 def _exec(command): | |
35 proc = subprocess.Popen(args=command, shell=True) | |
36 return_code = proc.wait() | |
37 if return_code != 0: | |
38 print "Error executing command [%s], return code is %d" % (command, return_code) | |
39 sys.exit(return_code) | |
40 | |
41 | |
42 def _parse_args(): | |
43 parser = OptionParser() | |
44 parser.add_option("-i", "--input") | |
45 parser.add_option("-o", "--output") | |
46 return parser.parse_args() | |
47 | |
48 | |
49 if __name__ == "__main__": | |
50 main() |