--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert_wrapper.py	Fri Apr 08 16:08:09 2016 -0400
@@ -0,0 +1,298 @@
+#!/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
+
+to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'mz5', '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 _add_filter(filters_file, contents):
+    filters_file.write("filter=%s\n" % contents)
+
+
+def _skip_line(options, file_num, line_parts):
+    file_num_column = options.filter_table_file_column
+    if not file_num_column:
+        return False
+    else:
+        target_file_num_val = str(file_num).strip()
+        query_file_num_val = line_parts[int(file_num_column) - 1].strip()
+        #print "target %s, query %s" % (target_file_num_val, query_file_num_val)
+        return target_file_num_val != query_file_num_val
+
+
+def _read_table_numbers(path, options, file_num=None):
+    unique_numbers = set([])
+    column_num = options.filter_table_column
+    input = open(path, "r")
+    first_line = True
+    for line in input:
+        if not line:
+            continue
+        line = line.strip()
+        if line.startswith("#"):
+            first_line = False
+            continue
+        if column_num == None:
+            column = line
+        else:
+            line_parts = line.split("\t")
+            if _skip_line(options, file_num, line_parts):
+                continue
+            column = line_parts[int(column_num) - 1]
+        match = re.match("\d+", column)
+        if match:
+            unique_numbers.add(int(match.group()))
+        first_line = False
+    return unique_numbers
+
+
+def shellquote(s):
+    return '"' + s.replace('"', '\\"') + '"'
+
+
+def _add_filter_line_from_file(filter_file, options, file_num=None):
+    file = options.filter_table
+    if not file:
+        return
+    numbers = _read_table_numbers(file, options, file_num)
+    msconvert_int_set = " ".join([str(number) for number in numbers])
+    filter_type = options.filter_table_type
+    if filter_type == 'number':
+        filter_prefix = 'scanNumber'
+    else:
+        filter_prefix = 'index'
+    _add_filter(filter_file, "%s %s" % (filter_prefix, msconvert_int_set))
+
+
+def _create_filters_file(options, file_num=None, debug=False):
+    suffix = "" if not file_num else str(file_num)
+    filters_file_path = "filters%s" % suffix
+    filters_file = open(filters_file_path, "w")
+    if options.filters_file:
+        filters_file.write(open(options.filters_file, "r").read())
+    for filter in options.filter:
+        _add_filter(filters_file, filter)
+    _add_filter_line_from_file(filters_file, options, file_num=file_num)
+
+    filters_file.close()
+    if debug:
+        print(( open(filters_file_path, "r").read() ))
+    return filters_file_path
+
+
+def _build_base_cmd(options,args=None):
+    to_extension = options.toextension
+    if to_extension.startswith("unindexed_"):
+        to_extension = to_extension[len("unindexed_"):]
+        to_params = "--noindex"
+    else:
+        to_params = ""
+    cmd = "msconvert --%s %s" % (to_extension, to_params)
+    if args:
+        cmd = "%s %s" % (cmd, ' '.join(args))
+    if str_to_bool(options.zlib):
+        cmd = "%s %s" % (cmd, "--zlib")
+    if options.binaryencoding:
+        cmd = "%s --%s" % (cmd, options.binaryencoding)
+    if options.mzencoding:
+        cmd = "%s --mz%s" % (cmd, options.mzencoding)
+    if options.intensityencoding:
+        cmd = "%s --inten%s" % (cmd, options.intensityencoding)
+    return cmd
+
+
+def _run(base_cmd, output_dir='output', inputs=[], debug=False):
+    inputs_as_str = " ".join(['%s' % shellquote(input) for input in inputs])
+    os.mkdir(output_dir)
+    cmd = "%s -o %s %s" % (base_cmd, shellquote(output_dir), inputs_as_str)
+    if debug:
+        print(cmd)
+    execute(cmd)
+    output_files = os.listdir(output_dir)
+    assert len(output_files) == 1
+    output_file = output_files[0]
+    return os.path.join(output_dir, output_file)
+
+
+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 msconvert command line.')
+    parser.add_option('--ident', dest='idents', action='append', default=[])
+    parser.add_option('--ident_name', dest='ident_names', action='append', default=[])
+    parser.add_option('--output', dest='output')
+    parser.add_option('--refinement', dest='refinement')
+    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('--zlib', dest='zlib', default="false")
+    parser.add_option('--filter', dest='filter', action='append', default=[])
+    parser.add_option('--filters_file', dest='filters_file', default=None)
+    parser.add_option('--filter_table', default=None)
+    parser.add_option('--filter_table_type', default='index', choices=['index', 'number'])
+    parser.add_option('--filter_table_column', default=None)
+    parser.add_option('--filter_table_file_column', default=None)
+    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 msconvert 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('.%s' % 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 in options.implicits:
+            continue
+        input_files.append(input_file)
+    for i, ident in enumerate(options.idents):
+        ident_file = options.ident_names[i]
+        copy_to_working_directory(ident, ident_file)
+
+    cmd = _build_base_cmd(options,args=args)
+    file_column = options.filter_table_file_column
+    if not file_column:
+        # Apply same filters to all files, just create a unviersal filter files
+        # and run msconvert once.
+        filters_file_path = _create_filters_file(options, debug=options.debug)
+        cmd = "%s -c %s" % (cmd, filters_file_path)
+    else:
+        # Dispatching on a column to filter different files differently, need to filter
+        # each input once with msconvert and then merge once.
+        filtered_files = []
+        for index, input_file in enumerate(input_files):
+            filters_file_path = _create_filters_file(options, index + 1, debug=options.debug)
+            filter_cmd = "%s -c %s" % (cmd, filters_file_path)
+            filtered_output_file = _run(filter_cmd, output_dir='output%d' % index, inputs=[input_file], debug=options.debug)
+            filtered_files.append(filtered_output_file)
+        input_files = filtered_files
+    if len(input_files) > 1:
+        cmd = "%s --merge" % cmd
+    output_file = _run(cmd, output_dir='output', inputs=input_files, debug=options.debug)
+    shutil.copy(output_file, options.output)
+    if options.refinement:
+        # .mzRefinement.tsv
+        files = os.listdir(os.getcwd())
+        for fname in files:
+            if fname.endswith('.mzRefinement.tsv'):
+                shutil.copy(fname, options.refinement)
+                break
+
+def __main__():
+    run_script()
+
+if __name__ == '__main__':
+    __main__()