Mercurial > repos > galaxyp > peptideshaker
comparison reverse.py @ 2:fb591fc7241c draft
Improved some datatype handling
| author | galaxyp |
|---|---|
| date | Thu, 20 Jun 2013 11:02:36 -0400 |
| parents | |
| children |
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| 1:7a74818e0eeb | 2:fb591fc7241c |
|---|---|
| 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() |