2 Provide access to information stored in the GERALD directory.
4 from datetime import datetime, date
11 from gaworkflow.pipeline.runfolder import \
16 from gaworkflow.util.ethelp import indent, flatten
20 Capture meaning out of the GERALD directory
24 RUN_PARAMETERS='RunParameters'
27 class LaneParameters(object):
29 Make it easy to access elements of LaneSpecificRunParameters from python
31 def __init__(self, gerald, key):
35 def __get_attribute(self, xml_tag):
36 subtree = self._gerald.tree.find('LaneSpecificRunParameters')
37 container = subtree.find(xml_tag)
38 if container is None or \
39 len(container.getchildren()) != LANES_PER_FLOWCELL:
40 raise RuntimeError('GERALD config.xml file changed')
41 lanes = [x.tag.split('_')[1] for x in container.getchildren()]
42 index = lanes.index(self._key)
43 #element = container.find(self._key)
44 element = container[index]
46 def _get_analysis(self):
47 return self.__get_attribute('ANALYSIS')
48 analysis = property(_get_analysis)
50 def _get_eland_genome(self):
51 return self.__get_attribute('ELAND_GENOME')
52 eland_genome = property(_get_eland_genome)
54 def _get_read_length(self):
55 return self.__get_attribute('READ_LENGTH')
56 read_length = property(_get_read_length)
58 def _get_use_bases(self):
59 return self.__get_attribute('USE_BASES')
60 use_bases = property(_get_use_bases)
62 class LaneSpecificRunParameters(object):
64 Provide access to LaneSpecificRunParameters
66 def __init__(self, gerald):
69 def __getitem__(self, key):
70 return Gerald.LaneParameters(self._gerald, key)
72 if self._keys is None:
73 tree = self._gerald.tree
74 analysis = tree.find('LaneSpecificRunParameters/ANALYSIS')
75 # according to the pipeline specs I think their fields
76 # are sampleName_laneID, with sampleName defaulting to s
77 # since laneIDs are constant lets just try using
79 self._keys = [ x.tag.split('_')[1] for x in analysis]
82 return [ self[x] for x in self.keys() ]
84 return zip(self.keys(), self.values())
86 return len(self.keys())
88 def __init__(self, xml=None):
92 # parse lane parameters out of the config.xml file
93 self.lanes = Gerald.LaneSpecificRunParameters(self)
96 self.eland_results = None
99 self.set_elements(xml)
102 if self.tree is None:
103 return datetime.today()
104 timestamp = self.tree.findtext('ChipWideRunParameters/TIME_STAMP')
105 epochstamp = time.mktime(time.strptime(timestamp, '%c'))
106 return datetime.fromtimestamp(epochstamp)
107 date = property(_get_date)
110 return time.mktime(self.date.timetuple())
111 time = property(_get_time, doc='return run time as seconds since epoch')
113 def _get_version(self):
114 if self.tree is None:
116 return self.tree.findtext('ChipWideRunParameters/SOFTWARE_VERSION')
117 version = property(_get_version)
121 Debugging function, report current object
123 print 'Gerald version:', self.version
124 print 'Gerald run date:', self.date
125 print 'Gerald config.xml:', self.tree
128 def get_elements(self):
129 if self.tree is None or self.summary is None:
132 gerald = ElementTree.Element(Gerald.GERALD,
133 {'version': unicode(Gerald.XML_VERSION)})
134 gerald.append(self.tree)
135 gerald.append(self.summary.get_elements())
136 if self.eland_results:
137 gerald.append(self.eland_results.get_elements())
140 def set_elements(self, tree):
141 if tree.tag != Gerald.GERALD:
142 raise ValueError('exptected GERALD')
143 xml_version = int(tree.attrib.get('version', 0))
144 if xml_version > Gerald.XML_VERSION:
145 logging.warn('XML tree is a higher version than this class')
146 for element in list(tree):
147 tag = element.tag.lower()
148 if tag == Gerald.RUN_PARAMETERS.lower():
150 elif tag == Gerald.SUMMARY.lower():
151 self.summary = Summary(xml=element)
152 elif tag == ELAND.ELAND.lower():
153 self.eland_results = ELAND(xml=element)
155 logging.warn("Unrecognized tag %s" % (element.tag,))
158 def gerald(pathname):
160 g.pathname = pathname
161 path, name = os.path.split(pathname)
162 config_pathname = os.path.join(pathname, 'config.xml')
163 g.tree = ElementTree.parse(config_pathname).getroot()
165 # parse Summary.htm file
166 summary_pathname = os.path.join(pathname, 'Summary.htm')
167 g.summary = Summary(summary_pathname)
169 g.eland_results = eland(g.pathname, g)
174 Convert a value to int if its an int otherwise a float.
178 except ValueError, e:
182 def parse_mean_range(value):
184 Parse values like 123 +/- 4.5
186 if value.strip() == 'unknown':
189 average, pm, deviation = value.split()
191 raise RuntimeError("Summary.htm file format changed")
192 return tonumber(average), tonumber(deviation)
194 def make_mean_range_element(parent, name, mean, deviation):
196 Make an ElementTree subelement <Name mean='mean', deviation='deviation'/>
198 element = ElementTree.SubElement(parent, name,
199 { 'mean': unicode(mean),
200 'deviation': unicode(deviation)})
203 def parse_mean_range_element(element):
205 Grab mean/deviation out of element
207 return (tonumber(element.attrib['mean']),
208 tonumber(element.attrib['deviation']))
210 class Summary(object):
212 Extract some useful information from the Summary.htm file
217 class LaneResultSummary(object):
219 Parse the LaneResultSummary table out of Summary.htm
220 Mostly for the cluster number
222 LANE_RESULT_SUMMARY = 'LaneResultSummary'
224 'Cluster': 'cluster',
225 'AverageFirstCycleIntensity': 'average_first_cycle_intensity',
226 'PercentIntensityAfter20Cycles': 'percent_intensity_after_20_cycles',
227 'PercentPassFilterClusters': 'percent_pass_filter_clusters',
228 'PercentPassFilterAlign': 'percent_pass_filter_align',
229 'AverageAlignmentScore': 'average_alignment_score',
230 'PercentErrorRate': 'percent_error_rate'
233 def __init__(self, html=None, xml=None):
236 self.average_first_cycle_intensity = None
237 self.percent_intensity_after_20_cycles = None
238 self.percent_pass_filter_clusters = None
239 self.percent_pass_filter_align = None
240 self.average_alignment_score = None
241 self.percent_error_rate = None
244 self.set_elements_from_html(html)
246 self.set_elements(xml)
248 def set_elements_from_html(self, row_element):
249 data = [ flatten(x) for x in row_element ]
251 raise RuntimeError("Summary.htm file format changed")
254 self.cluster = parse_mean_range(data[1])
255 self.average_first_cycle_intensity = parse_mean_range(data[2])
256 self.percent_intensity_after_20_cycles = parse_mean_range(data[3])
257 self.percent_pass_filter_clusters = parse_mean_range(data[4])
258 self.percent_pass_filter_align = parse_mean_range(data[5])
259 self.average_alignment_score = parse_mean_range(data[6])
260 self.percent_error_rate = parse_mean_range(data[7])
262 def get_elements(self):
263 lane_result = ElementTree.Element(
264 Summary.LaneResultSummary.LANE_RESULT_SUMMARY,
266 for tag, variable_name in Summary.LaneResultSummary.TAGS.items():
267 element = make_mean_range_element(
270 *getattr(self, variable_name)
274 def set_elements(self, tree):
275 if tree.tag != Summary.LaneResultSummary.LANE_RESULT_SUMMARY:
276 raise ValueError('Expected %s' % (
277 Summary.LaneResultSummary.LANE_RESULT_SUMMARY))
278 self.lane = tree.attrib['lane']
279 tags = Summary.LaneResultSummary.TAGS
280 for element in list(tree):
282 variable_name = tags[element.tag]
283 setattr(self, variable_name,
284 parse_mean_range_element(element))
286 logging.warn('Unrecognized tag %s' % (element.tag,))
288 def __init__(self, filename=None, xml=None):
289 self.lane_results = {}
291 if filename is not None:
292 self._extract_lane_results(filename)
294 self.set_elements(xml)
296 def __getitem__(self, key):
297 return self.lane_results[key]
300 return len(self.lane_results)
303 return self.lane_results.keys()
306 return self.lane_results.values()
309 return self.lane_results.items()
311 def _extract_lane_results(self, pathname):
313 extract the Lane Results Summary table
315 tree = ElementTree.parse(pathname).getroot()
316 if flatten(tree.findall('*//h2')[3]) != 'Lane Results Summary':
317 raise RuntimeError("Summary.htm file format changed")
319 tables = tree.findall('*//table')
321 # parse lane result summary
322 lane_summary = tables[2]
323 rows = lane_summary.getchildren()
324 headers = rows[0].getchildren()
325 if flatten(headers[2]) != 'Av 1st Cycle Int ':
326 raise RuntimeError("Summary.htm file format changed")
329 lrs = Summary.LaneResultSummary(html=r)
330 self.lane_results[lrs.lane] = lrs
332 def get_elements(self):
333 summary = ElementTree.Element(Summary.SUMMARY,
334 {'version': unicode(Summary.XML_VERSION)})
335 for lane in self.lane_results.values():
336 summary.append(lane.get_elements())
339 def set_elements(self, tree):
340 if tree.tag != Summary.SUMMARY:
341 return ValueError("Expected %s" % (Summary.SUMMARY,))
342 xml_version = int(tree.attrib.get('version', 0))
343 if xml_version > Summary.XML_VERSION:
344 logging.warn('Summary XML tree is a higher version than this class')
345 for element in list(tree):
346 lrs = Summary.LaneResultSummary()
347 lrs.set_elements(element)
348 self.lane_results[lrs.lane] = lrs
352 Debugging function, report current object
357 def build_genome_fasta_map(genome_dir):
358 # build fasta to fasta file map
359 genome = genome_dir.split(os.path.sep)[-1]
361 for vld_file in glob(os.path.join(genome_dir, '*.vld')):
363 if os.path.islink(vld_file):
365 vld_file = os.path.realpath(vld_file)
366 path, vld_name = os.path.split(vld_file)
367 name, ext = os.path.splitext(vld_name)
369 fasta_map[name] = name
371 fasta_map[name] = os.path.join(genome, name)
374 class ElandLane(object):
376 Process an eland result file
380 GENOME_MAP = 'GenomeMap'
381 GENOME_ITEM = 'GenomeItem'
382 MAPPED_READS = 'MappedReads'
383 MAPPED_ITEM = 'MappedItem'
384 MATCH_CODES = 'MatchCodes'
388 def __init__(self, pathname=None, genome_map=None, xml=None):
389 self.pathname = pathname
391 self._mapped_reads = {}
392 self._match_codes = {}
393 if genome_map is None:
395 self.genome_map = genome_map
397 if pathname is not None:
400 self.set_elements(xml)
404 Actually read the file and actually count the reads
406 # can't do anything if we don't have a file to process
407 if self.pathname is None:
410 if os.stat(self.pathname)[stat.ST_SIZE] == 0:
411 raise RuntimeError("Eland isn't done, try again later.")
416 match_codes = {'NM':0, 'QC':0, 'RM':0,
417 'U0':0, 'U1':0, 'U2':0,
418 'R0':0, 'R1':0, 'R2':0,
420 for line in open(self.pathname):
422 fields = line.split()
424 # match_codes[code] = match_codes.setdefault(code, 0) + 1
425 # the QC/NM etc codes are in the 3rd field and always present
426 match_codes[fields[2]] += 1
427 # ignore lines that don't have a fasta filename
430 fasta = self.genome_map.get(fields[6], fields[6])
431 mapped_reads[fasta] = mapped_reads.setdefault(fasta, 0) + 1
432 self._match_codes = match_codes
433 self._mapped_reads = mapped_reads
436 def _get_reads(self):
437 if self._reads is None:
440 reads = property(_get_reads)
442 def _get_mapped_reads(self):
443 if self._mapped_reads is None:
445 return self._mapped_reads
446 mapped_reads = property(_get_mapped_reads)
448 def _get_match_codes(self):
449 if self._match_codes is None:
451 return self._match_codes
452 match_codes = property(_get_match_codes)
454 def get_elements(self):
455 lane = ElementTree.Element(ElandLane.LANE,
457 unicode(ElandLane.XML_VERSION)})
458 genome_map = ElementTree.SubElement(lane, ElandLane.GENOME_MAP)
459 for k, v in self.genome_map.items():
460 item = ElementTree.SubElement(
461 genome_map, ElandLane.GENOME_ITEM,
462 {'name':k, 'value':unicode(v)})
463 mapped_reads = ElementTree.SubElement(lane, ElandLane.MAPPED_READS)
464 for k, v in self.mapped_reads.items():
465 item = ElementTree.SubElement(
466 mapped_reads, ElandLane.MAPPED_ITEM,
467 {'name':k, 'value':unicode(v)})
468 match_codes = ElementTree.SubElement(lane, ElandLane.MATCH_CODES)
469 for k, v in self.match_codes.items():
470 item = ElementTree.SubElement(
471 match_codes, ElandLane.MATCH_ITEM,
472 {'name':k, 'value':unicode(v)})
473 reads = ElementTree.SubElement(lane, ElandLane.READS)
474 reads.text = unicode(self.reads)
478 def set_elements(self, tree):
479 if tree.tag != ElandLane.LANE:
480 raise ValueError('Exptecting %s' % (ElandLane.LANE,))
482 tag = element.tag.lower()
483 if tag == ElandLane.GENOME_MAP.lower():
484 for child in element:
485 name = child.attrib['name']
486 value = child.attrib['value']
487 self.genome_map[name] = value
488 elif tag == ElandLane.MAPPED_READS.lower():
489 for child in element:
490 name = child.attrib['name']
491 value = child.attrib['value']
492 self._mapped_reads[name] = int(value)
493 elif tag == ElandLane.MATCH_CODES.lower():
494 for child in element:
495 name = child.attrib['name']
496 value = int(child.attrib['value'])
497 self._match_codes[name] = value
498 elif tag == ElandLane.READS.lower():
499 self._reads = int(element.text)
501 logging.warn("ElandLane unrecognized tag %s" % (element.tag,))
506 Summarize information from eland files
510 ELAND = 'ElandCollection'
514 def __init__(self, xml=None):
515 # we need information from the gerald config.xml
519 self.set_elements(xml)
522 return len(self.results)
525 return self.results.keys()
528 return self.results.values()
531 return self.results.items()
533 def __getitem__(self, key):
534 return self.results[key]
536 def get_elements(self):
537 root = ElementTree.Element(ELAND.ELAND,
538 {'version': unicode(ELAND.XML_VERSION)})
539 for lane_id, lane in self.results.items():
540 eland_lane = lane.get_elements()
541 eland_lane.attrib[ELAND.LANE_ID] = unicode(lane_id)
542 root.append(eland_lane)
545 def set_elements(self, tree):
546 if tree.tag.lower() != ELAND.ELAND.lower():
547 raise ValueError('Expecting %s', ELAND.ELAND)
548 for element in list(tree):
549 lane_id = element.attrib[ELAND.LANE_ID]
550 lane = ElandLane(xml=element)
551 self.results[lane_id] = lane
553 def eland(basedir, gerald=None, genome_maps=None):
555 for pathname in glob(os.path.join(basedir, "*_eland_result.txt")):
556 # extract the sample name
557 path, name = os.path.split(pathname)
558 split_name = name.split('_')
559 sample_name = split_name[0]
560 lane_id = split_name[1]
562 if genome_maps is not None:
563 genome_map = genome_maps[lane_id]
564 elif gerald is not None:
565 genome_dir = gerald.lanes[lane_id].eland_genome
566 genome_map = build_genome_fasta_map(genome_dir)
570 eland_result = ElandLane(pathname, genome_map)
571 e.results[lane_id] = eland_result