--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert_raw_wrapper.py	Wed Dec 19 00:10:08 2012 -0500
@@ -0,0 +1,124 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import shutil 
+import subprocess
+import re
+from os.path import basename
+import logging
+
+assert sys.version_info[:2] >= ( 2, 6 )
+
+log = logging.getLogger(__name__)
+working_directory = os.getcwd()
+tmp_stderr_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stderr').name
+tmp_stdout_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stdout').name
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def read_stderr():
+    stderr = ''
+    if(os.path.exists(tmp_stderr_name)):
+        with open(tmp_stderr_name, 'rb') as tmp_stderr:
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read(buffsize)
+                    if not stderr or len(stderr) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+    return stderr
+    
+def execute(command, stdin=None):
+    with open(tmp_stderr_name, 'wb') as tmp_stderr:
+        with open(tmp_stdout_name, 'wb') as tmp_stdout:
+            proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
+            returncode = proc.wait()
+            if returncode != 0:
+                raise Exception, "Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())
+
+def delete_file(path):
+    if os.path.exists(path):
+        try:
+            os.remove(path)
+        except:
+            pass
+
+def delete_directory(directory):
+    if os.path.exists(directory):
+        try:
+            shutil.rmtree(directory)
+        except:
+            pass
+
+def symlink(source, link_name):
+    import platform
+    if platform.system() == 'Windows':
+        import win32file
+        win32file.CreateSymbolicLink(source, link_name, 1)
+    else:
+        os.symlink(source, link_name)
+
+
+def copy_to_working_directory(data_file, relative_path):
+    if os.path.abspath(data_file) != os.path.abspath(relative_path):
+        shutil.copy(data_file, relative_path)
+    return relative_path
+
+def __main__():
+    run_script()
+
+#ENDTEMPLATE
+
+to_extensions = ['mzML', 'mzXML', 'mgf', 'txt', 'ms2', 'cms2']
+
+def str_to_bool(v):
+    """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
+    return v.lower() in ["yes", "true", "t", "1"]
+
+
+def run_script():
+    parser = optparse.OptionParser()
+    parser.add_option('--input', dest='input')
+    parser.add_option('--output', dest='output')
+    parser.add_option('--fromextension', dest='fromextension')
+    parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
+    parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
+    parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
+    parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])
+    parser.add_option('--noindex', dest='noindex')
+    parser.add_option('--zlib', dest='zlib')
+    parser.add_option('--filter', dest='filter', action='append', default=[])
+
+    (options, args) = parser.parse_args()
+
+    filter_commands = ''
+    for filter in options.filter:
+        filter_commands = "%s --filter \"%s\"" % (filter_commands, filter)
+
+    input_file = 'input.%s' % options.fromextension
+    copy_to_working_directory(options.input, input_file)
+    os.mkdir('output')
+    cmd = "msconvert --%s -o output" % (options.toextension)
+    if str_to_bool(options.noindex):
+        cmd = "%s %s" % (cmd, "--noindex")
+    if str_to_bool(options.zlib):
+        cmd = "%s %s" % (cmd, "--zlib")
+    cmd = "%s --%s" % (cmd, options.binaryencoding)
+    cmd = "%s --mz%s" % (cmd, options.mzencoding)
+    cmd = "%s --inten%s" % (cmd, options.intensityencoding)
+    cmd = "%s %s" % (cmd, input_file)
+    cmd = "%s %s" % (cmd, filter_commands)
+    print cmd
+    execute(cmd)
+    output_files = os.listdir('output')
+    assert len(output_files) == 1
+    output_file = output_files[0]
+    shutil.copy(os.path.join('output', output_file), options.output)
+
+if __name__ == '__main__': __main__()