Mercurial > repos > galaxyp > maxquant
diff maxquant_wrapper.py @ 0:d4b6c9eae635 draft
Initial commit.
| author | galaxyp |
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| date | Fri, 10 May 2013 17:22:51 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_wrapper.py Fri May 10 17:22:51 2013 -0400 @@ -0,0 +1,787 @@ +#!/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__()