annotate maxquant_wrapper.py @ 0:d4b6c9eae635 draft

Initial commit.

#!/usr/bin/env python
import optparse
import os
import shutil
import sys
import tempfile
import subprocess
import logging
from string import Template
from xml.sax.saxutils import escape
import xml.etree.ElementTree as ET

log = logging.getLogger(__name__)

DEBUG = True

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(64000)
        print open(tmp_stdout_name, "r").read(64000)


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):
        shutil.copy(data_file, relative_path)
    return relative_path


def __main__():
    run_script()


## Lock File Stuff
## http://www.evanfosmark.com/2009/01/cross-platform-file-locking-support-in-python/
import os
import time
import errno


class FileLockException(Exception):
    pass


class FileLock(object):
    """ A file locking mechanism that has context-manager support so
        you can use it in a with statement. This should be relatively cross
        compatible as it doesn't rely on msvcrt or fcntl for the locking.
    """

    def __init__(self, file_name, timeout=10, delay=.05):
        """ Prepare the file locker. Specify the file to lock and optionally
            the maximum timeout and the delay between each attempt to lock.
        """
        self.is_locked = False
        self.lockfile = os.path.join(os.getcwd(), "%s.lock" % file_name)
        self.file_name = file_name
        self.timeout = timeout
        self.delay = delay

    def acquire(self):
        """ Acquire the lock, if possible. If the lock is in use, it check again
            every `wait` seconds. It does this until it either gets the lock or
            exceeds `timeout` number of seconds, in which case it throws
            an exception.
        """
        start_time = time.time()
        while True:
            try:
                self.fd = os.open(self.lockfile, os.O_CREAT | os.O_EXCL | os.O_RDWR)
                break
            except OSError as e:
                if e.errno != errno.EEXIST:
                    raise
                if (time.time() - start_time) >= self.timeout:
                    raise FileLockException("Timeout occured.")
                time.sleep(self.delay)
        self.is_locked = True

    def release(self):
        """ Get rid of the lock by deleting the lockfile.
            When working in a `with` statement, this gets automatically
            called at the end.
        """
        if self.is_locked:
            os.close(self.fd)
            os.unlink(self.lockfile)
            self.is_locked = False

    def __enter__(self):
        """ Activated when used in the with statement.
            Should automatically acquire a lock to be used in the with block.
        """
        if not self.is_locked:
            self.acquire()
        return self

    def __exit__(self, type, value, traceback):
        """ Activated at the end of the with statement.
            It automatically releases the lock if it isn't locked.
        """
        if self.is_locked:
            self.release()

    def __del__(self):
        """ Make sure that the FileLock instance doesn't leave a lockfile
            lying around.
        """
        self.release()

TEMPLATE = """<?xml version="1.0" encoding="utf-8"?>
<MaxQuantParams xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" runOnCluster="false" processFolder="$process_folder">
  $raw_file_info
  <experimentalDesignFilename/>
  <slicePeaks>$slice_peaks</slicePeaks>
  <tempFolder/>
  <ncores>$num_cores</ncores>
  <ionCountIntensities>false</ionCountIntensities>
  <maxFeatureDetectionCores>1</maxFeatureDetectionCores>
  <verboseColumnHeaders>false</verboseColumnHeaders>
  <minTime>NaN</minTime>
  <maxTime>NaN</maxTime>
  <calcPeakProperties>$calc_peak_properties</calcPeakProperties>
  <useOriginalPrecursorMz>$use_original_precursor_mz</useOriginalPrecursorMz>
  $fixed_mods
  <multiModificationSearch>$multi_modification_search</multiModificationSearch>
  <fastaFiles>$database</fastaFiles>
  <fastaFilesFirstSearch/>
  <fixedSearchFolder/>
  <advancedRatios>$advanced_ratios</advancedRatios>
  <rtShift>$rt_shift</rtShift>
  <fastLfq>$fast_lfq</fastLfq>
  <randomize>$randomize</randomize>
  <specialAas>$special_aas</specialAas>
  <includeContamiants>$include_contamiants</includeContamiants>
  <equalIl>$equal_il</equalIl>
  <topxWindow>100</topxWindow>
  <maxPeptideMass>$max_peptide_mass</maxPeptideMass>
  <reporterPif>$reporter_pif</reporterPif>
  <reporterFraction>$reporter_fraction</reporterFraction>
  <reporterBasePeakRatio>$reporter_base_peak_ratio</reporterBasePeakRatio>
  <scoreThreshold>$score_threshold</scoreThreshold>
  <filterAacounts>$filter_aacounts</filterAacounts>
  <secondPeptide>$second_peptide</secondPeptide>
  <matchBetweenRuns>$match_between_runs</matchBetweenRuns>
  <matchBetweenRunsFdr>$match_between_runs_fdr</matchBetweenRunsFdr>
  <reQuantify>$re_quantify</reQuantify>
  <dependentPeptides>$dependent_peptides</dependentPeptides>
  <dependentPeptideFdr>$dependent_peptide_fdr</dependentPeptideFdr>
  <dependentPeptideMassBin>$dependent_peptide_mass_bin</dependentPeptideMassBin>
  <labelFree>$label_free</labelFree>
  <lfqMinEdgesPerNode>$lfq_min_edges_per_node</lfqMinEdgesPerNode>
  <lfqAvEdgesPerNode>$lfq_av_edges_per_node</lfqAvEdgesPerNode>
  <hybridQuantification>$hybrid_quantification</hybridQuantification>
  <msmsConnection>$msms_connection</msmsConnection>
  <ibaq>$ibaq</ibaq>
  <msmsRecalibration>$msms_recalibration</msmsRecalibration>
  <ibaqLogFit>$ibaq_log_fit</ibaqLogFit>
  <razorProteinFdr>$razor_protein_fdr</razorProteinFdr>
  <calcSequenceTags>$calc_sequence_tags</calcSequenceTags>
  <deNovoVarMods>$de_novo_var_mods</deNovoVarMods>
  <massDifferenceSearch>$mass_difference_search</massDifferenceSearch>
  <minPepLen>$min_pep_len</minPepLen>
  <peptideFdr>$peptide_fdr</peptideFdr>
  <peptidePep>$peptide_pep</peptidePep>
  <proteinFdr>$protein_fdr</proteinFdr>
  <siteFdr>$site_fdr</siteFdr>
  <minPeptideLengthForUnspecificSearch>$min_peptide_length_for_unspecific_search</minPeptideLengthForUnspecificSearch>
  <maxPeptideLengthForUnspecificSearch>$max_peptide_length_for_unspecific_search</maxPeptideLengthForUnspecificSearch>
  <useNormRatiosForOccupancy>$use_norm_ratios_for_occupancy</useNormRatiosForOccupancy>
  <minPeptides>$min_peptides</minPeptides>
  <minRazorPeptides>$min_razor_peptides</minRazorPeptides>
  <minUniquePeptides>$min_unique_peptides</minUniquePeptides>
  <useCounterparts>$use_counterparts</useCounterparts>
  <minRatioCount>$min_ratio_count</minRatioCount>
  <lfqMinRatioCount>$lfq_min_ratio_count</lfqMinRatioCount>
  <restrictProteinQuantification>$restrict_protein_quantification</restrictProteinQuantification>
  $restrict_mods
  <matchingTimeWindow>$matching_time_window</matchingTimeWindow>
  <numberOfCandidatesMultiplexedMsms>$number_of_candidates_multiplexed_msms</numberOfCandidatesMultiplexedMsms>
  <numberOfCandidatesMsms>$number_of_candidates_msms</numberOfCandidatesMsms>
  <separateAasForSiteFdr>$separate_aas_for_site_fdr</separateAasForSiteFdr>
  <massDifferenceMods />
  <aifParams aifSilWeight="$aif_sil_weight"
             aifIsoWeight="$aif_iso_weight"
             aifTopx="$aif_topx"
             aifCorrelation="$aif_correlation"
             aifCorrelationFirstPass="$aif_correlation_first_pass"
             aifMinMass="$aif_min_mass"
             aifMsmsTol="$aif_msms_tol"
             aifSecondPass="$aif_second_pass"
             aifIterative="$aif_iterative"
             aifThresholdFdr="$aif_threhold_fdr" />
  <groups>
    <ParameterGroups>
      $group_params
    </ParameterGroups>
  </groups>
  <qcSettings>
    <qcSetting xsi:nil="true" />
  </qcSettings>
  <msmsParams>
    $ftms_fragment_settings
    $itms_fragment_settings
    $tof_fragment_settings
    $unknown_fragment_settings
  </msmsParams>
  <keepLowScoresMode>$keep_low_scores_mode</keepLowScoresMode>
  <msmsCentroidMode>$msms_centroid_mode</msmsCentroidMode>
  <quantMode>$quant_mode</quantMode>
  <siteQuantMode>$site_quant_mode</siteQuantMode>
  <groupParams>
    <groupParam>
      $group_params
    </groupParam>
  </groupParams>
</MaxQuantParams>
"""

GROUP_TEMPLATE = """
         <maxCharge>$max_charge</maxCharge>
         <lcmsRunType>$lcms_run_type</lcmsRunType>
         <msInstrument>$ms_instrument</msInstrument>
         <groupIndex>$group_index</groupIndex>
         <maxLabeledAa>$max_labeled_aa</maxLabeledAa>
         <maxNmods>$max_n_mods</maxNmods>
         <maxMissedCleavages>$max_missed_cleavages</maxMissedCleavages>
         <multiplicity>$multiplicity</multiplicity>
         <protease>$protease</protease>
         <proteaseFirstSearch>$protease</proteaseFirstSearch>
         <useProteaseFirstSearch>false</useProteaseFirstSearch>
         <useVariableModificationsFirstSearch>false</useVariableModificationsFirstSearch>
         $variable_mods
         $isobaric_labels
         <variableModificationsFirstSearch>
            <string>Oxidation (M)</string>
            <string>Acetyl (Protein N-term)</string>
         </variableModificationsFirstSearch>
         <hasAdditionalVariableModifications>false</hasAdditionalVariableModifications>
         <additionalVariableModifications>
            <ArrayOfString />
         </additionalVariableModifications>
         <additionalVariableModificationProteins>
            <ArrayOfString />
         </additionalVariableModificationProteins>
         <doMassFiltering>$do_mass_filtering</doMassFiltering>
         <firstSearchTol>$first_search_tol</firstSearchTol>
         <mainSearchTol>$main_search_tol</mainSearchTol>
         $labels
"""

#         <labels>
#            <string />
#            <string>Arg10; Lys8</string>
#         </labels>

fragment_settings = {
  "FTMS":    {"InPpm": "true", "Deisotope": "true", "Topx": "10", "HigherCharges": "true",
              "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true",
              "tolerance_value": "20", "tolerance_unit": "Ppm", "name": "FTMS"},
  "ITMS":    {"InPpm": "false", "Deisotope": "false", "Topx": "6", "HigherCharges": "true",
              "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true",
              "tolerance_value": "0.5", "tolerance_unit": "Dalton", "name": "ITMS"},
  "TOF":     {"InPpm": "false", "Deisotope": "true", "Topx": "10", "HigherCharges": "true",
              "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true",
              "tolerance_value": "0.1", "tolerance_unit": "Dalton", "name": "TOF"},
  "Unknown": {"InPpm": "false", "Deisotope": "false", "Topx": "6", "HigherCharges": "true",
              "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true",
              "tolerance_value": "0.5", "tolerance_unit": "Dalton", "name": "Unknown"},
}


def build_isobaric_labels(reporter_type):
    if not reporter_type:
        return "<isobaricLabels />"
    if reporter_type == "itraq_4plex":
        prefix = "iTRAQ4plex"
        mzs = [114, 115, 116, 117]
    elif reporter_type == "itraq_8plex":
        prefix = "iTRAQ8plex"
        mzs = [113, 114, 115, 116, 117, 118, 119, 121]
    elif reporter_type == "tmt_2plex":
        prefix = "TMT2plex"
        mzs = [126, 127]
    elif reporter_type == "tmt_6plex":
        prefix = "TMT6plex"
        mzs = [126, 127, 128, 129, 130, 131]
    else:
        raise Exception("Unknown reporter type - %s" % reporter_type)
    labels = ["%s-%s%d" % (prefix, term, mz) for term in ["Nter", "Lys"] for mz in mzs]
    return wrap(map(xml_string, labels), "isobaricLabels")


def parse_groups(inputs_file, group_parts=["num"], input_parts=["name", "path"]):
    inputs_lines = [line.strip() for line in open(inputs_file, "r").readlines()]
    inputs_lines = [line for line in inputs_lines if line and not line.startswith("#")]
    cur_group = None
    i = 0
    group_prefixes = ["%s:" % group_part  for group_part in group_parts]
    input_prefixes = ["%s:" % input_part for input_part in input_parts]
    groups = {}
    while i < len(inputs_lines):
        line = inputs_lines[i]
        if line.startswith(group_prefixes[0]):
            # Start new group
            cur_group = line[len(group_prefixes[0]):]
            group_data = {}
            for j, group_prefix in enumerate(group_prefixes):
                group_line = inputs_lines[i + j]
                group_data[group_parts[j]] = group_line[len(group_prefix):]
            i += len(group_prefixes)
        elif line.startswith(input_prefixes[0]):
            input = []
            for j, input_prefix in enumerate(input_prefixes):
                part_line = inputs_lines[i + j]
                part = part_line[len(input_prefixes[j]):]
                input.append(part)
            if cur_group not in groups:
                groups[cur_group] = {"group_data": group_data, "inputs": []}
            groups[cur_group]["inputs"].append(input)
            i += len(input_prefixes)
        else:
            # Skip empty line
            i += 1
    return groups


def add_fragment_options(parser):
    for name, options in fragment_settings.iteritems():
        for key, value in options.iteritems():
            option_key = ("%s_%s" % (name, key)).lower()
            parser.add_option("--%s" % option_key, default=value)


def update_fragment_settings(arg_options):
    for name, options in fragment_settings.iteritems():
        for key, value in options.iteritems():
            arg_option_key = ("%s_%s" % (name, key)).lower()
            options[key] = getattr(arg_options, arg_option_key)


def to_fragment_settings(name, values):
    """
    """

    fragment_settings_template = """
    <FragmentSpectrumSettings Name="$name" InPpm="$InPpm" Deisotope="$Deisotope"
     Topx="$Topx" HigherCharges="$HigherCharges" IncludeWater="$IncludeWater" IncludeAmmonia="$IncludeAmmonia"
     DependentLosses="$DependentLosses">
      <Tolerance>
        <Value>$tolerance_value</Value>
        <Unit>$tolerance_unit</Unit>
      </Tolerance>
    </FragmentSpectrumSettings>
    """
    safe_values = dict(values)
    for key, value in safe_values.iteritems():
        safe_values[key] = escape(value)
    return Template(fragment_settings_template).substitute(safe_values)


def get_file_paths(files):
    return wrap([xml_string(name) for name in files], "filePaths")


def get_file_names(file_names):
    return wrap([xml_string(name) for name in file_names], "fileNames")


def get_file_groups(file_groups):
    return wrap([xml_int(file_group) for file_group in file_groups], "paramGroups")


def wrap(values, tag):
    return "<%s>%s</%s>" % (tag, "".join(values), tag)


def xml_string(str):
    if str:
        return "<string>%s</string>" % escape(str)
    else:
        return "<string />"


def xml_int(value):
    return "<int>%d</int>" % int(value)


def get_properties(options):
    direct_properties = ["lcms_run_type",
                         "max_missed_cleavages",
                         "protease",
                         "first_search_tol",
                         "main_search_tol",
                         "max_n_mods",
                         "max_charge",
                         "max_labeled_aa",
                         "do_mass_filtering",
                         "calc_peak_properties",
                         "use_original_precursor_mz",
                         "multi_modification_search",
                         "keep_low_scores_mode",
                         "msms_centroid_mode",
                         "quant_mode",
                         "site_quant_mode",
                         "advanced_ratios",
                         "rt_shift",
                         "fast_lfq",
                         "randomize",
                         "aif_sil_weight",
                         "aif_iso_weight",
                         "aif_topx",
                         "aif_correlation",
                         "aif_correlation_first_pass",
                         "aif_min_mass",
                         "aif_msms_tol",
                         "aif_second_pass",
                         "aif_iterative",
                         "aif_threhold_fdr",
                         "restrict_protein_quantification",
                         "matching_time_window",
                         "number_of_candidates_multiplexed_msms",
                         "number_of_candidates_msms",
                         "separate_aas_for_site_fdr",
                         "special_aas",
                         "include_contamiants",
                         "equal_il",
                         "topx_window",
                         "max_peptide_mass",
                         "reporter_pif",
                         "reporter_fraction",
                         "reporter_base_peak_ratio",
                         "score_threshold",
                         "filter_aacounts",
                         "second_peptide",
                         "match_between_runs",
                         "match_between_runs_fdr",
                         "re_quantify",
                         "dependent_peptides",
                         "dependent_peptide_fdr",
                         "dependent_peptide_mass_bin",
                         "label_free",
                         "lfq_min_edges_per_node",
                         "lfq_av_edges_per_node",
                         "hybrid_quantification",
                         "msms_connection",
                         "ibaq",
                         "msms_recalibration",
                         "ibaq_log_fit",
                         "razor_protein_fdr",
                         "calc_sequence_tags",
                         "de_novo_var_mods",
                         "mass_difference_search",
                         "min_pep_len",
                         "peptide_fdr",
                         "peptide_pep",
                         "protein_fdr",
                         "site_fdr",
                         "min_peptide_length_for_unspecific_search",
                         "max_peptide_length_for_unspecific_search",
                         "use_norm_ratios_for_occupancy",
                         "min_peptides",
                         "min_razor_peptides",
                         "min_unique_peptides",
                         "use_counterparts",
                         "min_ratio_count",
                         "lfq_min_ratio_count",
                        ]

    props = {
      "slice_peaks": "true",
      "num_cores": str(options.num_cores),
      "database": xml_string(setup_database(options)),
      "process_folder": os.path.join(os.getcwd(), "process"),
    }
    for prop in direct_properties:
        props[prop] = str(getattr(options, prop))

    for name, fragment_options in fragment_settings.iteritems():
        key = "%s_fragment_settings" % name.lower()
        props[key] = to_fragment_settings(name, fragment_options)

    restrict_mods_string = wrap(map(xml_string, options.restrict_mods), "restrictMods")
    props["restrict_mods"] = restrict_mods_string
    fixed_mods_string = wrap(map(xml_string, options.fixed_mods), "fixedModifications")
    props["fixed_mods"] = fixed_mods_string
    variable_mods_string = wrap(map(xml_string, options.variable_mods), "variableModifications")
    props["variable_mods"] = variable_mods_string
    return props


# http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
def which(program):
    import os

    def is_exe(fpath):
        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)

    fpath, fname = os.path.split(program)
    if fpath:
        if is_exe(program):
            return program
    else:
        for path in os.environ["PATH"].split(os.pathsep):
            path = path.strip('"')
            exe_file = os.path.join(path, program)
            if is_exe(exe_file):
                return exe_file

    return None


def get_unique_path(base, extension):
    """
    """
    return "%s_%d%s" % (base, int(time.time() * 1000), extension)


def get_env_property(name, default):
    if name in os.environ:
        return os.environ[name]
    else:
        return default


def setup_database(options):
    database_path = options.database
    database_name = options.database_name
    database_name = database_name.replace(" ", "_")
    (database_basename, extension) = os.path.splitext(database_name)
    database_destination = get_unique_path(database_basename, ".fasta")
    assert database_destination == os.path.basename(database_destination)
    symlink(database_path, database_destination)

    database_conf = get_env_property("MAXQUANT_DATABASE_CONF", None)
    if not database_conf:
        exe_path = which("MaxQuantCmd.exe")
        database_conf = os.path.join(os.path.dirname(exe_path), "conf", "databases.xml")
    with FileLock(database_conf + ".galaxy_lock"):
        tree = ET.parse(database_conf)
        root = tree.getroot()
        databases_node = root.find("Databases")
        database_node = ET.SubElement(databases_node, 'databases')
        database_node.attrib["search_expression"] = ">([^ ]*)"
        database_node.attrib["replacement_expression"] = "%1"
        database_node.attrib["filename"] = database_destination
        tree.write(database_conf)
    return os.path.abspath(database_destination)


def setup_inputs(input_groups_path):
    parsed_groups = parse_groups(input_groups_path)
    paths = []
    names = []
    group_nums = []
    for group, group_info in parsed_groups.iteritems():
        files = group_info["inputs"]
        group_num = group_info["group_data"]["num"]
        for (name, path) in files:
            name = os.path.basename(name)
            if not name.lower().endswith(".raw"):
                name = "%s.%s" % (name, ".RAW")
            symlink(path, name)
            paths.append(os.path.abspath(name))
            names.append(os.path.splitext(name)[0])
            group_nums.append(group_num)
    file_data = (get_file_paths(paths), get_file_names(names), get_file_groups(group_nums))
    return "<rawFileInfo>%s%s%s<Fractions/><Values/></rawFileInfo> " % file_data


def set_group_params(properties, options):
    labels = [""]
    if options.labels:
        labels = options.labels
    labels_string = wrap([xml_string(label.replace(",", "; ")) for label in labels], "labels")
    group_properties = dict(properties)
    group_properties["labels"] = labels_string
    group_properties["multiplicity"] = len(labels)
    group_properties["group_index"] = "1"
    group_properties["ms_instrument"] = "0"
    group_params = Template(GROUP_TEMPLATE).substitute(group_properties)
    properties["group_params"] = group_params


def split_mods(mods_string):
    return [mod for mod in mods_string.split(",") if mod] if mods_string else []


def run_script():
    parser = optparse.OptionParser()
    parser.add_option("--input_groups")
    parser.add_option("--database")
    parser.add_option("--database_name")
    parser.add_option("--num_cores", type="int", default=4)
    parser.add_option("--max_missed_cleavages", type="int", default=2)
    parser.add_option("--protease", default="Trypsin/P")
    parser.add_option("--first_search_tol", default="20")
    parser.add_option("--main_search_tol", default="6")
    parser.add_option("--max_n_mods", type="int", default=5)
    parser.add_option("--max_charge", type="int", default=7)
    parser.add_option("--do_mass_filtering", default="true")
    parser.add_option("--labels", action="append", default=[])
    parser.add_option("--max_labeled_aa", type="int", default=3)
    parser.add_option("--keep_low_scores_mode", type="int", default=0)
    parser.add_option("--msms_centroid_mode", type="int", default=1)
    # 0 = all peptides, 1 = Use razor and unique peptides, 2 = use unique peptides
    parser.add_option("--quant_mode", type="int", default=1)
    parser.add_option("--site_quant_mode", type="int", default=0)
    parser.add_option("--aif_sil_weight", type="int", default=4)
    parser.add_option("--aif_iso_weight", type="int", default=2)
    parser.add_option("--aif_topx", type="int", default=50)
    parser.add_option("--aif_correlation", type="float", default=0.8)
    parser.add_option("--aif_correlation_first_pass", type="float", default=0.8)
    parser.add_option("--aif_min_mass", type="float", default=0)
    parser.add_option("--aif_msms_tol", type="float", default=10)
    parser.add_option("--aif_second_pass", default="false")
    parser.add_option("--aif_iterative", default="false")
    parser.add_option("--aif_threhold_fdr", default="0.01")
    parser.add_option("--restrict_protein_quantification", default="true")
    parser.add_option("--matching_time_window", default="2")
    parser.add_option("--number_of_candidates_multiplexed_msms", default="50")
    parser.add_option("--number_of_candidates_msms", default="15")
    parser.add_option("--separate_aas_for_site_fdr", default="true")
    parser.add_option("--advanced_ratios", default="false")
    parser.add_option("--rt_shift", default="false")
    parser.add_option("--fast_lfq", default="true")
    parser.add_option("--randomize", default="false")
    parser.add_option("--special_aas", default="KR")
    parser.add_option("--include_contamiants", default="false")
    parser.add_option("--equal_il", default="false")
    parser.add_option("--topx_window", default="100")
    parser.add_option("--max_peptide_mass", default="5000")
    parser.add_option("--reporter_pif", default="0.75")
    parser.add_option("--reporter_fraction", default="0")
    parser.add_option("--reporter_base_peak_ratio", default="0")
    parser.add_option("--score_threshold", default="0")
    parser.add_option("--filter_aacounts", default="true")
    parser.add_option("--second_peptide", default="true")
    parser.add_option("--match_between_runs", default="false")
    parser.add_option("--match_between_runs_fdr", default="false")
    parser.add_option("--re_quantify", default="true")
    parser.add_option("--dependent_peptides", default="false")
    parser.add_option("--dependent_peptide_fdr", default="0.01")
    parser.add_option("--dependent_peptide_mass_bin", default="0.0055")
    parser.add_option("--label_free", default="false")
    parser.add_option("--lfq_min_edges_per_node", default="3")
    parser.add_option("--lfq_av_edges_per_node", default="6")
    parser.add_option("--hybrid_quantification", default="false")
    parser.add_option("--msms_connection", default="false")
    parser.add_option("--ibaq", default="false")
    parser.add_option("--msms_recalibration", default="false")
    parser.add_option("--ibaq_log_fit", default="true")
    parser.add_option("--razor_protein_fdr", default="true")
    parser.add_option("--calc_sequence_tags", default="false")
    parser.add_option("--de_novo_var_mods", default="true")
    parser.add_option("--mass_difference_search", default="false")
    parser.add_option("--min_pep_len", default="7")
    parser.add_option("--peptide_fdr", default="0.01")
    parser.add_option("--peptide_pep", default="1")
    parser.add_option("--protein_fdr", default="0.01")
    parser.add_option("--site_fdr", default="0.01")
    parser.add_option("--min_peptide_length_for_unspecific_search", default="8")
    parser.add_option("--max_peptide_length_for_unspecific_search", default="25")
    parser.add_option("--use_norm_ratios_for_occupancy", default="true")
    parser.add_option("--min_peptides", default="1")
    parser.add_option("--min_razor_peptides", default="1")
    parser.add_option("--min_unique_peptides", default="0")
    parser.add_option("--use_counterparts", default="false")
    parser.add_option("--min_ratio_count", default="2")
    parser.add_option("--lfq_min_ratio_count", default="2")
    parser.add_option("--calc_peak_properties", default="false")
    parser.add_option("--use_original_precursor_mz", default="false")
    parser.add_option("--multi_modification_search", default="false")
    parser.add_option("--lcms_run_type", default="0")
    parser.add_option("--reporter_type", default=None)
    parser.add_option("--output_mqpar", default=None)
    text_outputs = {
                    "aif_msms": "aifMsms",
                    "all_peptides": "allPeptides",
                    "evidence": "evidence",
                    "modification_specific_peptides": "modificationSpecificPeptides",
                    "msms": "msms",
                    "msms_scans": "msmsScans",
                    "mz_range": "mzRange",
                    "parameters": "parameters",
                    "peptides": "peptides",
                    "protein_groups": "proteinGroups",
                    "sim_peptides": "simPeptides",
                    "sim_scans": "simScans",
                    "summary": "summary"
                   }
    for output in text_outputs.keys():
        parser.add_option("--output_%s" % output, default=None)

    parser.add_option("--variable_mods", default="Oxidation (M),Acetyl (Protein N-term)")
    parser.add_option("--restrict_mods", default="Oxidation (M),Acetyl (Protein N-term)")
    parser.add_option("--fixed_mods", default="Carbamidomethyl (C)")

    add_fragment_options(parser)

    (options, args) = parser.parse_args()
    options.restrict_mods = split_mods(options.restrict_mods)
    options.fixed_mods = split_mods(options.fixed_mods)
    options.variable_mods = split_mods(options.variable_mods)

    update_fragment_settings(options)

    raw_file_info = setup_inputs(options.input_groups)
    properties = get_properties(options)
    properties["raw_file_info"] = raw_file_info
    properties["isobaric_labels"] = build_isobaric_labels(options.reporter_type)
    set_group_params(properties, options)
    driver_contents = Template(TEMPLATE).substitute(properties)
    open("mqpar.xml", "w").write(driver_contents)
    print driver_contents
    execute("MaxQuantCmd.exe mqpar.xml %d" % options.num_cores)
    for key, basename in text_outputs.iteritems():
        attribute = "output_%s" % key
        destination = getattr(options, attribute, None)
        if destination:
            source = os.path.join("combined", "txt", "%s.txt" % basename)
            shutil.copy(source, destination)
    output_mqpar = options.output_mqpar
    if output_mqpar:
        shutil.copy("mqpar.xml", output_mqpar)

if __name__ == '__main__':
    __main__()