Mercurial > repos > galaxyp > maxquant

comparison maxquant_wrapper.py @ 0:d4b6c9eae635 draft

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Initial commit.
author galaxyp
date Fri, 10 May 2013 17:22:51 -0400
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-1:000000000000 0:d4b6c9eae635
1 #!/usr/bin/env python
2 import optparse
3 import os
4 import shutil
5 import sys
6 import tempfile
7 import subprocess
8 import logging
9 from string import Template
10 from xml.sax.saxutils import escape
11 import xml.etree.ElementTree as ET
12
13 log = logging.getLogger(__name__)
14
15 DEBUG = True
16
17 working_directory = os.getcwd()
18 tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stderr').name
19 tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name
20
21
22 def stop_err(msg):
23 sys.stderr.write("%s\n" % msg)
24 sys.exit()
25
26
27 def read_stderr():
28 stderr = ''
29 if(os.path.exists(tmp_stderr_name)):
30 with open(tmp_stderr_name, 'rb') as tmp_stderr:
31 buffsize = 1048576
32 try:
33 while True:
34 stderr += tmp_stderr.read(buffsize)
35 if not stderr or len(stderr) % buffsize != 0:
36 break
37 except OverflowError:
38 pass
39 return stderr
40
41
42 def execute(command, stdin=None):
43 try:
44 with open(tmp_stderr_name, 'wb') as tmp_stderr:
45 with open(tmp_stdout_name, 'wb') as tmp_stdout:
46 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
47 returncode = proc.wait()
48 if returncode != 0:
49 raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
50 finally:
51 print open(tmp_stderr_name, "r").read(64000)
52 print open(tmp_stdout_name, "r").read(64000)
53
54
55 def delete_file(path):
56 if os.path.exists(path):
57 try:
58 os.remove(path)
59 except:
60 pass
61
62
63 def delete_directory(directory):
64 if os.path.exists(directory):
65 try:
66 shutil.rmtree(directory)
67 except:
68 pass
69
70
71 def symlink(source, link_name):
72 import platform
73 if platform.system() == 'Windows':
74 try:
75 import win32file
76 win32file.CreateSymbolicLink(source, link_name, 1)
77 except:
78 shutil.copy(source, link_name)
79 else:
80 os.symlink(source, link_name)
81
82
83 def copy_to_working_directory(data_file, relative_path):
84 if os.path.abspath(data_file) != os.path.abspath(relative_path):
85 shutil.copy(data_file, relative_path)
86 return relative_path
87
88
89 def __main__():
90 run_script()
91
92
93 ## Lock File Stuff
94 ## http://www.evanfosmark.com/2009/01/cross-platform-file-locking-support-in-python/
95 import os
96 import time
97 import errno
98
99
100 class FileLockException(Exception):
101 pass
102
103
104 class FileLock(object):
105 """ A file locking mechanism that has context-manager support so
106 you can use it in a with statement. This should be relatively cross
107 compatible as it doesn't rely on msvcrt or fcntl for the locking.
108 """
109
110 def __init__(self, file_name, timeout=10, delay=.05):
111 """ Prepare the file locker. Specify the file to lock and optionally
112 the maximum timeout and the delay between each attempt to lock.
113 """
114 self.is_locked = False
115 self.lockfile = os.path.join(os.getcwd(), "%s.lock" % file_name)
116 self.file_name = file_name
117 self.timeout = timeout
118 self.delay = delay
119
120 def acquire(self):
121 """ Acquire the lock, if possible. If the lock is in use, it check again
122 every `wait` seconds. It does this until it either gets the lock or
123 exceeds `timeout` number of seconds, in which case it throws
124 an exception.
125 """
126 start_time = time.time()
127 while True:
128 try:
129 self.fd = os.open(self.lockfile, os.O_CREAT | os.O_EXCL | os.O_RDWR)
130 break
131 except OSError as e:
132 if e.errno != errno.EEXIST:
133 raise
134 if (time.time() - start_time) >= self.timeout:
135 raise FileLockException("Timeout occured.")
136 time.sleep(self.delay)
137 self.is_locked = True
138
139 def release(self):
140 """ Get rid of the lock by deleting the lockfile.
141 When working in a `with` statement, this gets automatically
142 called at the end.
143 """
144 if self.is_locked:
145 os.close(self.fd)
146 os.unlink(self.lockfile)
147 self.is_locked = False
148
149 def __enter__(self):
150 """ Activated when used in the with statement.
151 Should automatically acquire a lock to be used in the with block.
152 """
153 if not self.is_locked:
154 self.acquire()
155 return self
156
157 def __exit__(self, type, value, traceback):
158 """ Activated at the end of the with statement.
159 It automatically releases the lock if it isn't locked.
160 """
161 if self.is_locked:
162 self.release()
163
164 def __del__(self):
165 """ Make sure that the FileLock instance doesn't leave a lockfile
166 lying around.
167 """
168 self.release()
169
170 TEMPLATE = """<?xml version="1.0" encoding="utf-8"?>
171 <MaxQuantParams xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" runOnCluster="false" processFolder="$process_folder">
172 $raw_file_info
173 <experimentalDesignFilename/>
174 <slicePeaks>$slice_peaks</slicePeaks>
175 <tempFolder/>
176 <ncores>$num_cores</ncores>
177 <ionCountIntensities>false</ionCountIntensities>
178 <maxFeatureDetectionCores>1</maxFeatureDetectionCores>
179 <verboseColumnHeaders>false</verboseColumnHeaders>
180 <minTime>NaN</minTime>
181 <maxTime>NaN</maxTime>
182 <calcPeakProperties>$calc_peak_properties</calcPeakProperties>
183 <useOriginalPrecursorMz>$use_original_precursor_mz</useOriginalPrecursorMz>
184 $fixed_mods
185 <multiModificationSearch>$multi_modification_search</multiModificationSearch>
186 <fastaFiles>$database</fastaFiles>
187 <fastaFilesFirstSearch/>
188 <fixedSearchFolder/>
189 <advancedRatios>$advanced_ratios</advancedRatios>
190 <rtShift>$rt_shift</rtShift>
191 <fastLfq>$fast_lfq</fastLfq>
192 <randomize>$randomize</randomize>
193 <specialAas>$special_aas</specialAas>
194 <includeContamiants>$include_contamiants</includeContamiants>
195 <equalIl>$equal_il</equalIl>
196 <topxWindow>100</topxWindow>
197 <maxPeptideMass>$max_peptide_mass</maxPeptideMass>
198 <reporterPif>$reporter_pif</reporterPif>
199 <reporterFraction>$reporter_fraction</reporterFraction>
200 <reporterBasePeakRatio>$reporter_base_peak_ratio</reporterBasePeakRatio>
201 <scoreThreshold>$score_threshold</scoreThreshold>
202 <filterAacounts>$filter_aacounts</filterAacounts>
203 <secondPeptide>$second_peptide</secondPeptide>
204 <matchBetweenRuns>$match_between_runs</matchBetweenRuns>
205 <matchBetweenRunsFdr>$match_between_runs_fdr</matchBetweenRunsFdr>
206 <reQuantify>$re_quantify</reQuantify>
207 <dependentPeptides>$dependent_peptides</dependentPeptides>
208 <dependentPeptideFdr>$dependent_peptide_fdr</dependentPeptideFdr>
209 <dependentPeptideMassBin>$dependent_peptide_mass_bin</dependentPeptideMassBin>
210 <labelFree>$label_free</labelFree>
211 <lfqMinEdgesPerNode>$lfq_min_edges_per_node</lfqMinEdgesPerNode>
212 <lfqAvEdgesPerNode>$lfq_av_edges_per_node</lfqAvEdgesPerNode>
213 <hybridQuantification>$hybrid_quantification</hybridQuantification>
214 <msmsConnection>$msms_connection</msmsConnection>
215 <ibaq>$ibaq</ibaq>
216 <msmsRecalibration>$msms_recalibration</msmsRecalibration>
217 <ibaqLogFit>$ibaq_log_fit</ibaqLogFit>
218 <razorProteinFdr>$razor_protein_fdr</razorProteinFdr>
219 <calcSequenceTags>$calc_sequence_tags</calcSequenceTags>
220 <deNovoVarMods>$de_novo_var_mods</deNovoVarMods>
221 <massDifferenceSearch>$mass_difference_search</massDifferenceSearch>
222 <minPepLen>$min_pep_len</minPepLen>
223 <peptideFdr>$peptide_fdr</peptideFdr>
224 <peptidePep>$peptide_pep</peptidePep>
225 <proteinFdr>$protein_fdr</proteinFdr>
226 <siteFdr>$site_fdr</siteFdr>
227 <minPeptideLengthForUnspecificSearch>$min_peptide_length_for_unspecific_search</minPeptideLengthForUnspecificSearch>
228 <maxPeptideLengthForUnspecificSearch>$max_peptide_length_for_unspecific_search</maxPeptideLengthForUnspecificSearch>
229 <useNormRatiosForOccupancy>$use_norm_ratios_for_occupancy</useNormRatiosForOccupancy>
230 <minPeptides>$min_peptides</minPeptides>
231 <minRazorPeptides>$min_razor_peptides</minRazorPeptides>
232 <minUniquePeptides>$min_unique_peptides</minUniquePeptides>
233 <useCounterparts>$use_counterparts</useCounterparts>
234 <minRatioCount>$min_ratio_count</minRatioCount>
235 <lfqMinRatioCount>$lfq_min_ratio_count</lfqMinRatioCount>
236 <restrictProteinQuantification>$restrict_protein_quantification</restrictProteinQuantification>
237 $restrict_mods
238 <matchingTimeWindow>$matching_time_window</matchingTimeWindow>
239 <numberOfCandidatesMultiplexedMsms>$number_of_candidates_multiplexed_msms</numberOfCandidatesMultiplexedMsms>
240 <numberOfCandidatesMsms>$number_of_candidates_msms</numberOfCandidatesMsms>
241 <separateAasForSiteFdr>$separate_aas_for_site_fdr</separateAasForSiteFdr>
242 <massDifferenceMods />
243 <aifParams aifSilWeight="$aif_sil_weight"
244 aifIsoWeight="$aif_iso_weight"
245 aifTopx="$aif_topx"
246 aifCorrelation="$aif_correlation"
247 aifCorrelationFirstPass="$aif_correlation_first_pass"
248 aifMinMass="$aif_min_mass"
249 aifMsmsTol="$aif_msms_tol"
250 aifSecondPass="$aif_second_pass"
251 aifIterative="$aif_iterative"
252 aifThresholdFdr="$aif_threhold_fdr" />
253 <groups>
254 <ParameterGroups>
255 $group_params
256 </ParameterGroups>
257 </groups>
258 <qcSettings>
259 <qcSetting xsi:nil="true" />
260 </qcSettings>
261 <msmsParams>
262 $ftms_fragment_settings
263 $itms_fragment_settings
264 $tof_fragment_settings
265 $unknown_fragment_settings
266 </msmsParams>
267 <keepLowScoresMode>$keep_low_scores_mode</keepLowScoresMode>
268 <msmsCentroidMode>$msms_centroid_mode</msmsCentroidMode>
269 <quantMode>$quant_mode</quantMode>
270 <siteQuantMode>$site_quant_mode</siteQuantMode>
271 <groupParams>
272 <groupParam>
273 $group_params
274 </groupParam>
275 </groupParams>
276 </MaxQuantParams>
277 """
278
279 GROUP_TEMPLATE = """
280 <maxCharge>$max_charge</maxCharge>
281 <lcmsRunType>$lcms_run_type</lcmsRunType>
282 <msInstrument>$ms_instrument</msInstrument>
283 <groupIndex>$group_index</groupIndex>
284 <maxLabeledAa>$max_labeled_aa</maxLabeledAa>
285 <maxNmods>$max_n_mods</maxNmods>
286 <maxMissedCleavages>$max_missed_cleavages</maxMissedCleavages>
287 <multiplicity>$multiplicity</multiplicity>
288 <protease>$protease</protease>
289 <proteaseFirstSearch>$protease</proteaseFirstSearch>
290 <useProteaseFirstSearch>false</useProteaseFirstSearch>
291 <useVariableModificationsFirstSearch>false</useVariableModificationsFirstSearch>
292 $variable_mods
293 $isobaric_labels
294 <variableModificationsFirstSearch>
295 <string>Oxidation (M)</string>
296 <string>Acetyl (Protein N-term)</string>
297 </variableModificationsFirstSearch>
298 <hasAdditionalVariableModifications>false</hasAdditionalVariableModifications>
299 <additionalVariableModifications>
300 <ArrayOfString />
301 </additionalVariableModifications>
302 <additionalVariableModificationProteins>
303 <ArrayOfString />
304 </additionalVariableModificationProteins>
305 <doMassFiltering>$do_mass_filtering</doMassFiltering>
306 <firstSearchTol>$first_search_tol</firstSearchTol>
307 <mainSearchTol>$main_search_tol</mainSearchTol>
308 $labels
309 """
310
311 # <labels>
312 # <string />
313 # <string>Arg10; Lys8</string>
314 # </labels>
315
316 fragment_settings = {
317 "FTMS": {"InPpm": "true", "Deisotope": "true", "Topx": "10", "HigherCharges": "true",
318 "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true",
319 "tolerance_value": "20", "tolerance_unit": "Ppm", "name": "FTMS"},
320 "ITMS": {"InPpm": "false", "Deisotope": "false", "Topx": "6", "HigherCharges": "true",
321 "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true",
322 "tolerance_value": "0.5", "tolerance_unit": "Dalton", "name": "ITMS"},
323 "TOF": {"InPpm": "false", "Deisotope": "true", "Topx": "10", "HigherCharges": "true",
324 "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true",
325 "tolerance_value": "0.1", "tolerance_unit": "Dalton", "name": "TOF"},
326 "Unknown": {"InPpm": "false", "Deisotope": "false", "Topx": "6", "HigherCharges": "true",
327 "IncludeWater": "true", "IncludeAmmonia": "true", "DependentLosses": "true",
328 "tolerance_value": "0.5", "tolerance_unit": "Dalton", "name": "Unknown"},
329 }
330
331
332 def build_isobaric_labels(reporter_type):
333 if not reporter_type:
334 return "<isobaricLabels />"
335 if reporter_type == "itraq_4plex":
336 prefix = "iTRAQ4plex"
337 mzs = [114, 115, 116, 117]
338 elif reporter_type == "itraq_8plex":
339 prefix = "iTRAQ8plex"
340 mzs = [113, 114, 115, 116, 117, 118, 119, 121]
341 elif reporter_type == "tmt_2plex":
342 prefix = "TMT2plex"
343 mzs = [126, 127]
344 elif reporter_type == "tmt_6plex":
345 prefix = "TMT6plex"
346 mzs = [126, 127, 128, 129, 130, 131]
347 else:
348 raise Exception("Unknown reporter type - %s" % reporter_type)
349 labels = ["%s-%s%d" % (prefix, term, mz) for term in ["Nter", "Lys"] for mz in mzs]
350 return wrap(map(xml_string, labels), "isobaricLabels")
351
352
353 def parse_groups(inputs_file, group_parts=["num"], input_parts=["name", "path"]):
354 inputs_lines = [line.strip() for line in open(inputs_file, "r").readlines()]
355 inputs_lines = [line for line in inputs_lines if line and not line.startswith("#")]
356 cur_group = None
357 i = 0
358 group_prefixes = ["%s:" % group_part for group_part in group_parts]
359 input_prefixes = ["%s:" % input_part for input_part in input_parts]
360 groups = {}
361 while i < len(inputs_lines):
362 line = inputs_lines[i]
363 if line.startswith(group_prefixes[0]):
364 # Start new group
365 cur_group = line[len(group_prefixes[0]):]
366 group_data = {}
367 for j, group_prefix in enumerate(group_prefixes):
368 group_line = inputs_lines[i + j]
369 group_data[group_parts[j]] = group_line[len(group_prefix):]
370 i += len(group_prefixes)
371 elif line.startswith(input_prefixes[0]):
372 input = []
373 for j, input_prefix in enumerate(input_prefixes):
374 part_line = inputs_lines[i + j]
375 part = part_line[len(input_prefixes[j]):]
376 input.append(part)
377 if cur_group not in groups:
378 groups[cur_group] = {"group_data": group_data, "inputs": []}
379 groups[cur_group]["inputs"].append(input)
380 i += len(input_prefixes)
381 else:
382 # Skip empty line
383 i += 1
384 return groups
385
386
387 def add_fragment_options(parser):
388 for name, options in fragment_settings.iteritems():
389 for key, value in options.iteritems():
390 option_key = ("%s_%s" % (name, key)).lower()
391 parser.add_option("--%s" % option_key, default=value)
392
393
394 def update_fragment_settings(arg_options):
395 for name, options in fragment_settings.iteritems():
396 for key, value in options.iteritems():
397 arg_option_key = ("%s_%s" % (name, key)).lower()
398 options[key] = getattr(arg_options, arg_option_key)
399
400
401 def to_fragment_settings(name, values):
402 """
403 """
404
405 fragment_settings_template = """
406 <FragmentSpectrumSettings Name="$name" InPpm="$InPpm" Deisotope="$Deisotope"
407 Topx="$Topx" HigherCharges="$HigherCharges" IncludeWater="$IncludeWater" IncludeAmmonia="$IncludeAmmonia"
408 DependentLosses="$DependentLosses">
409 <Tolerance>
410 <Value>$tolerance_value</Value>
411 <Unit>$tolerance_unit</Unit>
412 </Tolerance>
413 </FragmentSpectrumSettings>
414 """
415 safe_values = dict(values)
416 for key, value in safe_values.iteritems():
417 safe_values[key] = escape(value)
418 return Template(fragment_settings_template).substitute(safe_values)
419
420
421 def get_file_paths(files):
422 return wrap([xml_string(name) for name in files], "filePaths")
423
424
425 def get_file_names(file_names):
426 return wrap([xml_string(name) for name in file_names], "fileNames")
427
428
429 def get_file_groups(file_groups):
430 return wrap([xml_int(file_group) for file_group in file_groups], "paramGroups")
431
432
433 def wrap(values, tag):
434 return "<%s>%s</%s>" % (tag, "".join(values), tag)
435
436
437 def xml_string(str):
438 if str:
439 return "<string>%s</string>" % escape(str)
440 else:
441 return "<string />"
442
443
444 def xml_int(value):
445 return "<int>%d</int>" % int(value)
446
447
448 def get_properties(options):
449 direct_properties = ["lcms_run_type",
450 "max_missed_cleavages",
451 "protease",
452 "first_search_tol",
453 "main_search_tol",
454 "max_n_mods",
455 "max_charge",
456 "max_labeled_aa",
457 "do_mass_filtering",
458 "calc_peak_properties",
459 "use_original_precursor_mz",
460 "multi_modification_search",
461 "keep_low_scores_mode",
462 "msms_centroid_mode",
463 "quant_mode",
464 "site_quant_mode",
465 "advanced_ratios",
466 "rt_shift",
467 "fast_lfq",
468 "randomize",
469 "aif_sil_weight",
470 "aif_iso_weight",
471 "aif_topx",
472 "aif_correlation",
473 "aif_correlation_first_pass",
474 "aif_min_mass",
475 "aif_msms_tol",
476 "aif_second_pass",
477 "aif_iterative",
478 "aif_threhold_fdr",
479 "restrict_protein_quantification",
480 "matching_time_window",
481 "number_of_candidates_multiplexed_msms",
482 "number_of_candidates_msms",
483 "separate_aas_for_site_fdr",
484 "special_aas",
485 "include_contamiants",
486 "equal_il",
487 "topx_window",
488 "max_peptide_mass",
489 "reporter_pif",
490 "reporter_fraction",
491 "reporter_base_peak_ratio",
492 "score_threshold",
493 "filter_aacounts",
494 "second_peptide",
495 "match_between_runs",
496 "match_between_runs_fdr",
497 "re_quantify",
498 "dependent_peptides",
499 "dependent_peptide_fdr",
500 "dependent_peptide_mass_bin",
501 "label_free",
502 "lfq_min_edges_per_node",
503 "lfq_av_edges_per_node",
504 "hybrid_quantification",
505 "msms_connection",
506 "ibaq",
507 "msms_recalibration",
508 "ibaq_log_fit",
509 "razor_protein_fdr",
510 "calc_sequence_tags",
511 "de_novo_var_mods",
512 "mass_difference_search",
513 "min_pep_len",
514 "peptide_fdr",
515 "peptide_pep",
516 "protein_fdr",
517 "site_fdr",
518 "min_peptide_length_for_unspecific_search",
519 "max_peptide_length_for_unspecific_search",
520 "use_norm_ratios_for_occupancy",
521 "min_peptides",
522 "min_razor_peptides",
523 "min_unique_peptides",
524 "use_counterparts",
525 "min_ratio_count",
526 "lfq_min_ratio_count",
527 ]
528
529 props = {
530 "slice_peaks": "true",
531 "num_cores": str(options.num_cores),
532 "database": xml_string(setup_database(options)),
533 "process_folder": os.path.join(os.getcwd(), "process"),
534 }
535 for prop in direct_properties:
536 props[prop] = str(getattr(options, prop))
537
538 for name, fragment_options in fragment_settings.iteritems():
539 key = "%s_fragment_settings" % name.lower()
540 props[key] = to_fragment_settings(name, fragment_options)
541
542 restrict_mods_string = wrap(map(xml_string, options.restrict_mods), "restrictMods")
543 props["restrict_mods"] = restrict_mods_string
544 fixed_mods_string = wrap(map(xml_string, options.fixed_mods), "fixedModifications")
545 props["fixed_mods"] = fixed_mods_string
546 variable_mods_string = wrap(map(xml_string, options.variable_mods), "variableModifications")
547 props["variable_mods"] = variable_mods_string
548 return props
549
550
551 # http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
552 def which(program):
553 import os
554
555 def is_exe(fpath):
556 return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
557
558 fpath, fname = os.path.split(program)
559 if fpath:
560 if is_exe(program):
561 return program
562 else:
563 for path in os.environ["PATH"].split(os.pathsep):
564 path = path.strip('"')
565 exe_file = os.path.join(path, program)
566 if is_exe(exe_file):
567 return exe_file
568
569 return None
570
571
572 def get_unique_path(base, extension):
573 """
574 """
575 return "%s_%d%s" % (base, int(time.time() * 1000), extension)
576
577
578 def get_env_property(name, default):
579 if name in os.environ:
580 return os.environ[name]
581 else:
582 return default
583
584
585 def setup_database(options):
586 database_path = options.database
587 database_name = options.database_name
588 database_name = database_name.replace(" ", "_")
589 (database_basename, extension) = os.path.splitext(database_name)
590 database_destination = get_unique_path(database_basename, ".fasta")
591 assert database_destination == os.path.basename(database_destination)
592 symlink(database_path, database_destination)
593
594 database_conf = get_env_property("MAXQUANT_DATABASE_CONF", None)
595 if not database_conf:
596 exe_path = which("MaxQuantCmd.exe")
597 database_conf = os.path.join(os.path.dirname(exe_path), "conf", "databases.xml")
598 with FileLock(database_conf + ".galaxy_lock"):
599 tree = ET.parse(database_conf)
600 root = tree.getroot()
601 databases_node = root.find("Databases")
602 database_node = ET.SubElement(databases_node, 'databases')
603 database_node.attrib["search_expression"] = ">([^ ]*)"
604 database_node.attrib["replacement_expression"] = "%1"
605 database_node.attrib["filename"] = database_destination
606 tree.write(database_conf)
607 return os.path.abspath(database_destination)
608
609
610 def setup_inputs(input_groups_path):
611 parsed_groups = parse_groups(input_groups_path)
612 paths = []
613 names = []
614 group_nums = []
615 for group, group_info in parsed_groups.iteritems():
616 files = group_info["inputs"]
617 group_num = group_info["group_data"]["num"]
618 for (name, path) in files:
619 name = os.path.basename(name)
620 if not name.lower().endswith(".raw"):
621 name = "%s.%s" % (name, ".RAW")
622 symlink(path, name)
623 paths.append(os.path.abspath(name))
624 names.append(os.path.splitext(name)[0])
625 group_nums.append(group_num)
626 file_data = (get_file_paths(paths), get_file_names(names), get_file_groups(group_nums))
627 return "<rawFileInfo>%s%s%s<Fractions/><Values/></rawFileInfo> " % file_data
628
629
630 def set_group_params(properties, options):
631 labels = [""]
632 if options.labels:
633 labels = options.labels
634 labels_string = wrap([xml_string(label.replace(",", "; ")) for label in labels], "labels")
635 group_properties = dict(properties)
636 group_properties["labels"] = labels_string
637 group_properties["multiplicity"] = len(labels)
638 group_properties["group_index"] = "1"
639 group_properties["ms_instrument"] = "0"
640 group_params = Template(GROUP_TEMPLATE).substitute(group_properties)
641 properties["group_params"] = group_params
642
643
644 def split_mods(mods_string):
645 return [mod for mod in mods_string.split(",") if mod] if mods_string else []
646
647
648 def run_script():
649 parser = optparse.OptionParser()
650 parser.add_option("--input_groups")
651 parser.add_option("--database")
652 parser.add_option("--database_name")
653 parser.add_option("--num_cores", type="int", default=4)
654 parser.add_option("--max_missed_cleavages", type="int", default=2)
655 parser.add_option("--protease", default="Trypsin/P")
656 parser.add_option("--first_search_tol", default="20")
657 parser.add_option("--main_search_tol", default="6")
658 parser.add_option("--max_n_mods", type="int", default=5)
659 parser.add_option("--max_charge", type="int", default=7)
660 parser.add_option("--do_mass_filtering", default="true")
661 parser.add_option("--labels", action="append", default=[])
662 parser.add_option("--max_labeled_aa", type="int", default=3)
663 parser.add_option("--keep_low_scores_mode", type="int", default=0)
664 parser.add_option("--msms_centroid_mode", type="int", default=1)
665 # 0 = all peptides, 1 = Use razor and unique peptides, 2 = use unique peptides
666 parser.add_option("--quant_mode", type="int", default=1)
667 parser.add_option("--site_quant_mode", type="int", default=0)
668 parser.add_option("--aif_sil_weight", type="int", default=4)
669 parser.add_option("--aif_iso_weight", type="int", default=2)
670 parser.add_option("--aif_topx", type="int", default=50)
671 parser.add_option("--aif_correlation", type="float", default=0.8)
672 parser.add_option("--aif_correlation_first_pass", type="float", default=0.8)
673 parser.add_option("--aif_min_mass", type="float", default=0)
674 parser.add_option("--aif_msms_tol", type="float", default=10)
675 parser.add_option("--aif_second_pass", default="false")
676 parser.add_option("--aif_iterative", default="false")
677 parser.add_option("--aif_threhold_fdr", default="0.01")
678 parser.add_option("--restrict_protein_quantification", default="true")
679 parser.add_option("--matching_time_window", default="2")
680 parser.add_option("--number_of_candidates_multiplexed_msms", default="50")
681 parser.add_option("--number_of_candidates_msms", default="15")
682 parser.add_option("--separate_aas_for_site_fdr", default="true")
683 parser.add_option("--advanced_ratios", default="false")
684 parser.add_option("--rt_shift", default="false")
685 parser.add_option("--fast_lfq", default="true")
686 parser.add_option("--randomize", default="false")
687 parser.add_option("--special_aas", default="KR")
688 parser.add_option("--include_contamiants", default="false")
689 parser.add_option("--equal_il", default="false")
690 parser.add_option("--topx_window", default="100")
691 parser.add_option("--max_peptide_mass", default="5000")
692 parser.add_option("--reporter_pif", default="0.75")
693 parser.add_option("--reporter_fraction", default="0")
694 parser.add_option("--reporter_base_peak_ratio", default="0")
695 parser.add_option("--score_threshold", default="0")
696 parser.add_option("--filter_aacounts", default="true")
697 parser.add_option("--second_peptide", default="true")
698 parser.add_option("--match_between_runs", default="false")
699 parser.add_option("--match_between_runs_fdr", default="false")
700 parser.add_option("--re_quantify", default="true")
701 parser.add_option("--dependent_peptides", default="false")
702 parser.add_option("--dependent_peptide_fdr", default="0.01")
703 parser.add_option("--dependent_peptide_mass_bin", default="0.0055")
704 parser.add_option("--label_free", default="false")
705 parser.add_option("--lfq_min_edges_per_node", default="3")
706 parser.add_option("--lfq_av_edges_per_node", default="6")
707 parser.add_option("--hybrid_quantification", default="false")
708 parser.add_option("--msms_connection", default="false")
709 parser.add_option("--ibaq", default="false")
710 parser.add_option("--msms_recalibration", default="false")
711 parser.add_option("--ibaq_log_fit", default="true")
712 parser.add_option("--razor_protein_fdr", default="true")
713 parser.add_option("--calc_sequence_tags", default="false")
714 parser.add_option("--de_novo_var_mods", default="true")
715 parser.add_option("--mass_difference_search", default="false")
716 parser.add_option("--min_pep_len", default="7")
717 parser.add_option("--peptide_fdr", default="0.01")
718 parser.add_option("--peptide_pep", default="1")
719 parser.add_option("--protein_fdr", default="0.01")
720 parser.add_option("--site_fdr", default="0.01")
721 parser.add_option("--min_peptide_length_for_unspecific_search", default="8")
722 parser.add_option("--max_peptide_length_for_unspecific_search", default="25")
723 parser.add_option("--use_norm_ratios_for_occupancy", default="true")
724 parser.add_option("--min_peptides", default="1")
725 parser.add_option("--min_razor_peptides", default="1")
726 parser.add_option("--min_unique_peptides", default="0")
727 parser.add_option("--use_counterparts", default="false")
728 parser.add_option("--min_ratio_count", default="2")
729 parser.add_option("--lfq_min_ratio_count", default="2")
730 parser.add_option("--calc_peak_properties", default="false")
731 parser.add_option("--use_original_precursor_mz", default="false")
732 parser.add_option("--multi_modification_search", default="false")
733 parser.add_option("--lcms_run_type", default="0")
734 parser.add_option("--reporter_type", default=None)
735 parser.add_option("--output_mqpar", default=None)
736 text_outputs = {
737 "aif_msms": "aifMsms",
738 "all_peptides": "allPeptides",
739 "evidence": "evidence",
740 "modification_specific_peptides": "modificationSpecificPeptides",
741 "msms": "msms",
742 "msms_scans": "msmsScans",
743 "mz_range": "mzRange",
744 "parameters": "parameters",
745 "peptides": "peptides",
746 "protein_groups": "proteinGroups",
747 "sim_peptides": "simPeptides",
748 "sim_scans": "simScans",
749 "summary": "summary"
750 }
751 for output in text_outputs.keys():
752 parser.add_option("--output_%s" % output, default=None)
753
754 parser.add_option("--variable_mods", default="Oxidation (M),Acetyl (Protein N-term)")
755 parser.add_option("--restrict_mods", default="Oxidation (M),Acetyl (Protein N-term)")
756 parser.add_option("--fixed_mods", default="Carbamidomethyl (C)")
757
758 add_fragment_options(parser)
759
760 (options, args) = parser.parse_args()
761 options.restrict_mods = split_mods(options.restrict_mods)
762 options.fixed_mods = split_mods(options.fixed_mods)
763 options.variable_mods = split_mods(options.variable_mods)
764
765 update_fragment_settings(options)
766
767 raw_file_info = setup_inputs(options.input_groups)
768 properties = get_properties(options)
769 properties["raw_file_info"] = raw_file_info
770 properties["isobaric_labels"] = build_isobaric_labels(options.reporter_type)
771 set_group_params(properties, options)
772 driver_contents = Template(TEMPLATE).substitute(properties)
773 open("mqpar.xml", "w").write(driver_contents)
774 print driver_contents
775 execute("MaxQuantCmd.exe mqpar.xml %d" % options.num_cores)
776 for key, basename in text_outputs.iteritems():
777 attribute = "output_%s" % key
778 destination = getattr(options, attribute, None)
779 if destination:
780 source = os.path.join("combined", "txt", "%s.txt" % basename)
781 shutil.copy(source, destination)
782 output_mqpar = options.output_mqpar
783 if output_mqpar:
784 shutil.copy("mqpar.xml", output_mqpar)
785
786 if __name__ == '__main__':
787 __main__()