--- a/msconvert_wrapper.py	Fri Apr 08 16:01:32 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,298 +0,0 @@
-#!/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__()