--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ms_data_converter.py	Wed Mar 11 11:36:26 2015 -0400
@@ -0,0 +1,157 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import shutil
+import subprocess
+import re
+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):
+    try:
+        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()))
+    finally:
+        print(( open(tmp_stderr_name, "r").read() ))
+        print(( open(tmp_stdout_name, "r").read() ))
+
+
+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':
+        try:
+            import win32file
+            win32file.CreateSymbolicLink(source, link_name, 1)
+        except:
+            shutil.copy(source, link_name)
+    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):
+        symlink(data_file, relative_path)
+    return relative_path
+
+
+def __main__():
+    run_script()
+
+#ENDTEMPLATE
+
+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 shellquote(s):
+    return '"' + s.replace('"', '\\"') + '"'
+
+def run_script():
+    parser = optparse.OptionParser()
+    parser.add_option('--input', dest='inputs', action='append', default=[])
+    parser.add_option('--input_name', dest='input_names', action='append', default=[])
+    parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the AB SCIEX MS Data Converter command line.')
+    parser.add_option('--output', dest='output')
+    parser.add_option('--fromextension', dest='fromextension')
+    parser.add_option('--toextension', dest='toextension', default='mzML', choices=['mzML', 'mgf'])
+    parser.add_option('--content_type', dest='content_type', default='centroid', choices=['profile', 'centroid', 'proteinpilot'])
+    parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
+    parser.add_option('--zlib', dest='zlib', default="false")
+    parser.add_option('--index', dest='index', default="false")
+    parser.add_option('--debug', dest='debug', action='store_true', default=False)
+
+    (options, args) = parser.parse_args()
+    if len(options.inputs) < 1:
+        stop_err("No input files to ms_data_convert specified")
+    if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):
+        stop_err("Number(s) of supplied input names and input files do not match")
+    if not options.output:
+        stop_err("Must specify output location")
+    input_files = []
+    for i, input in enumerate(options.inputs):
+        input_base = None
+        if len(options.input_names) > i:
+            input_base = options.input_names[i]
+            input_base = input_base.replace("'", "").replace("\"", "")
+            print("1- input_base: %s" % input_base)
+        if not input_base:
+            input_base = 'input%s' % i
+            print("2- input_base: %s" % input_base)
+        if not input_base.lower().endswith(options.fromextension.lower()) and input not in options.implicits:
+            input_file = '%s.%s' % (input_base, options.fromextension)
+            print("3- input_base: %s" % input_base)
+            print("3- input_file: %s" % input_file)
+        else:
+            input_file = input_base
+            print("4- input_base: %s" % input_base)
+            print("4- input_file: %s" % input_file)
+        input_file = input_file
+        copy_to_working_directory(input, input_file)
+        if input not in options.implicits:
+            input_files.append(input_file)
+    ## AB_SCIEX_MS_Converter <input format> <input data> <output content type> <output format> <output file> [data compression setting] [data precision setting] [create index flag]
+    inputs_as_str = " ".join(['%s' % shellquote(input) for input in input_files])
+    output_file = re.sub('(%s)?$' % options.fromextension.lower(), options.toextension, input_files[0].lower())
+    cmd = "AB_SCIEX_MS_Converter %s %s %s %s %s" % (options.fromextension.upper(), inputs_as_str, options.content_type, options.toextension.upper(), output_file )
+    if str_to_bool(options.zlib):
+        cmd = "%s %s" % (cmd, "/zlib")
+    if options.binaryencoding:
+        cmd = "%s %s" % (cmd, "/singleprecision" if options.binaryencoding == '32' else "/doubleprecision")
+    if str_to_bool(options.zlib):
+        cmd = "%s %s" % (cmd, "/index")
+    if options.debug:
+        print(cmd)
+    execute(cmd)
+    shutil.copy(output_file, options.output)
+
+if __name__ == '__main__':
+    __main__()