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 return datetime.strptime(timestamp, '%c')
106 date = property(_get_date)
109 return time.mktime(self.date.timetuple())
110 time = property(_get_time, doc='return run time as seconds since epoch')
112 def _get_version(self):
113 if self.tree is None:
115 return self.tree.findtext('ChipWideRunParameters/SOFTWARE_VERSION')
116 version = property(_get_version)
120 Debugging function, report current object
122 print 'Gerald version:', self.version
123 print 'Gerald run date:', self.date
124 print 'Gerald config.xml:', self.tree
127 def get_elements(self):
128 if self.tree is None or self.summary is None:
131 gerald = ElementTree.Element(Gerald.GERALD,
132 {'version': unicode(Gerald.XML_VERSION)})
133 gerald.append(self.tree)
134 gerald.append(self.summary.get_elements())
135 if self.eland_results:
136 gerald.append(self.eland_results.get_elements())
139 def set_elements(self, tree):
140 if tree.tag != Gerald.GERALD:
141 raise ValueError('exptected GERALD')
142 xml_version = int(tree.attrib.get('version', 0))
143 if xml_version > Gerald.XML_VERSION:
144 logging.warn('XML tree is a higher version than this class')
145 for element in list(tree):
146 tag = element.tag.lower()
147 if tag == Gerald.RUN_PARAMETERS.lower():
149 elif tag == Gerald.SUMMARY.lower():
150 self.summary = Summary(xml=element)
151 elif tag == ELAND.ELAND.lower():
152 self.eland_results = ELAND(xml=element)
154 logging.warn("Unrecognized tag %s" % (element.tag,))
157 def gerald(pathname):
159 g.pathname = pathname
160 path, name = os.path.split(pathname)
161 config_pathname = os.path.join(pathname, 'config.xml')
162 g.tree = ElementTree.parse(config_pathname).getroot()
164 # parse Summary.htm file
165 summary_pathname = os.path.join(pathname, 'Summary.htm')
166 g.summary = Summary(summary_pathname)
168 g.eland_results = eland(g.pathname, g)
173 Convert a value to int if its an int otherwise a float.
177 except ValueError, e:
181 def parse_mean_range(value):
183 Parse values like 123 +/- 4.5
185 if value.strip() == 'unknown':
188 average, pm, deviation = value.split()
190 raise RuntimeError("Summary.htm file format changed")
191 return tonumber(average), tonumber(deviation)
193 def make_mean_range_element(parent, name, mean, deviation):
195 Make an ElementTree subelement <Name mean='mean', deviation='deviation'/>
197 element = ElementTree.SubElement(parent, name,
198 { 'mean': unicode(mean),
199 'deviation': unicode(deviation)})
202 def parse_mean_range_element(element):
204 Grab mean/deviation out of element
206 return (tonumber(element.attrib['mean']),
207 tonumber(element.attrib['deviation']))
209 class Summary(object):
211 Extract some useful information from the Summary.htm file
216 class LaneResultSummary(object):
218 Parse the LaneResultSummary table out of Summary.htm
219 Mostly for the cluster number
221 LANE_RESULT_SUMMARY = 'LaneResultSummary'
223 'Cluster': 'cluster',
224 'AverageFirstCycleIntensity': 'average_first_cycle_intensity',
225 'PercentIntensityAfter20Cycles': 'percent_intensity_after_20_cycles',
226 'PercentPassFilterClusters': 'percent_pass_filter_clusters',
227 'PercentPassFilterAlign': 'percent_pass_filter_align',
228 'AverageAlignmentScore': 'average_alignment_score',
229 'PercentErrorRate': 'percent_error_rate'
232 def __init__(self, html=None, xml=None):
235 self.average_first_cycle_intensity = None
236 self.percent_intensity_after_20_cycles = None
237 self.percent_pass_filter_clusters = None
238 self.percent_pass_filter_align = None
239 self.average_alignment_score = None
240 self.percent_error_rate = None
243 self.set_elements_from_html(html)
245 self.set_elements(xml)
247 def set_elements_from_html(self, row_element):
248 data = [ flatten(x) for x in row_element ]
250 raise RuntimeError("Summary.htm file format changed")
253 self.cluster = parse_mean_range(data[1])
254 self.average_first_cycle_intensity = parse_mean_range(data[2])
255 self.percent_intensity_after_20_cycles = parse_mean_range(data[3])
256 self.percent_pass_filter_clusters = parse_mean_range(data[4])
257 self.percent_pass_filter_align = parse_mean_range(data[5])
258 self.average_alignment_score = parse_mean_range(data[6])
259 self.percent_error_rate = parse_mean_range(data[7])
261 def get_elements(self):
262 lane_result = ElementTree.Element(
263 Summary.LaneResultSummary.LANE_RESULT_SUMMARY,
265 for tag, variable_name in Summary.LaneResultSummary.TAGS.items():
266 element = make_mean_range_element(
269 *getattr(self, variable_name)
273 def set_elements(self, tree):
274 if tree.tag != Summary.LaneResultSummary.LANE_RESULT_SUMMARY:
275 raise ValueError('Expected %s' % (
276 Summary.LaneResultSummary.LANE_RESULT_SUMMARY))
277 self.lane = tree.attrib['lane']
278 tags = Summary.LaneResultSummary.TAGS
279 for element in list(tree):
281 variable_name = tags[element.tag]
282 setattr(self, variable_name,
283 parse_mean_range_element(element))
285 logging.warn('Unrecognized tag %s' % (element.tag,))
287 def __init__(self, filename=None, xml=None):
288 self.lane_results = {}
290 if filename is not None:
291 self._extract_lane_results(filename)
293 self.set_elements(xml)
295 def __getitem__(self, key):
296 return self.lane_results[key]
299 return len(self.lane_results)
302 return self.lane_results.keys()
305 return self.lane_results.values()
308 return self.lane_results.items()
310 def _extract_lane_results(self, pathname):
312 extract the Lane Results Summary table
314 tree = ElementTree.parse(pathname).getroot()
315 if flatten(tree.findall('*//h2')[3]) != 'Lane Results Summary':
316 raise RuntimeError("Summary.htm file format changed")
318 tables = tree.findall('*//table')
320 # parse lane result summary
321 lane_summary = tables[2]
322 rows = lane_summary.getchildren()
323 headers = rows[0].getchildren()
324 if flatten(headers[2]) != 'Av 1st Cycle Int ':
325 raise RuntimeError("Summary.htm file format changed")
328 lrs = Summary.LaneResultSummary(html=r)
329 self.lane_results[lrs.lane] = lrs
331 def get_elements(self):
332 summary = ElementTree.Element(Summary.SUMMARY,
333 {'version': unicode(Summary.XML_VERSION)})
334 for lane in self.lane_results.values():
335 summary.append(lane.get_elements())
338 def set_elements(self, tree):
339 if tree.tag != Summary.SUMMARY:
340 return ValueError("Expected %s" % (Summary.SUMMARY,))
341 xml_version = int(tree.attrib.get('version', 0))
342 if xml_version > Summary.XML_VERSION:
343 logging.warn('Summary XML tree is a higher version than this class')
344 for element in list(tree):
345 lrs = Summary.LaneResultSummary()
346 lrs.set_elements(element)
347 self.lane_results[lrs.lane] = lrs
351 Debugging function, report current object
356 def build_genome_fasta_map(genome_dir):
357 # build fasta to fasta file map
358 genome = genome_dir.split(os.path.sep)[-1]
360 for vld_file in glob(os.path.join(genome_dir, '*.vld')):
362 if os.path.islink(vld_file):
364 vld_file = os.path.realpath(vld_file)
365 path, vld_name = os.path.split(vld_file)
366 name, ext = os.path.splitext(vld_name)
368 fasta_map[name] = name
370 fasta_map[name] = os.path.join(genome, name)
373 class ElandLane(object):
375 Process an eland result file
379 GENOME_MAP = 'GenomeMap'
380 GENOME_ITEM = 'GenomeItem'
381 MAPPED_READS = 'MappedReads'
382 MAPPED_ITEM = 'MappedItem'
383 MATCH_CODES = 'MatchCodes'
387 def __init__(self, pathname=None, genome_map=None, xml=None):
388 self.pathname = pathname
390 self._mapped_reads = {}
391 self._match_codes = {}
392 if genome_map is None:
394 self.genome_map = genome_map
396 if pathname is not None:
399 self.set_elements(xml)
403 Actually read the file and actually count the reads
405 # can't do anything if we don't have a file to process
406 if self.pathname is None:
409 if os.stat(self.pathname)[stat.ST_SIZE] == 0:
410 raise RuntimeError("Eland isn't done, try again later.")
415 match_codes = {'NM':0, 'QC':0, 'RM':0,
416 'U0':0, 'U1':0, 'U2':0,
417 'R0':0, 'R1':0, 'R2':0,
419 for line in open(self.pathname):
421 fields = line.split()
423 # match_codes[code] = match_codes.setdefault(code, 0) + 1
424 # the QC/NM etc codes are in the 3rd field and always present
425 match_codes[fields[2]] += 1
426 # ignore lines that don't have a fasta filename
429 fasta = self.genome_map.get(fields[6], fields[6])
430 mapped_reads[fasta] = mapped_reads.setdefault(fasta, 0) + 1
431 self._match_codes = match_codes
432 self._mapped_reads = mapped_reads
435 def _get_reads(self):
436 if self._reads is None:
439 reads = property(_get_reads)
441 def _get_mapped_reads(self):
442 if self._mapped_reads is None:
444 return self._mapped_reads
445 mapped_reads = property(_get_mapped_reads)
447 def _get_match_codes(self):
448 if self._match_codes is None:
450 return self._match_codes
451 match_codes = property(_get_match_codes)
453 def get_elements(self):
454 lane = ElementTree.Element(ElandLane.LANE,
456 unicode(ElandLane.XML_VERSION)})
457 genome_map = ElementTree.SubElement(lane, ElandLane.GENOME_MAP)
458 for k, v in self.genome_map.items():
459 item = ElementTree.SubElement(
460 genome_map, ElandLane.GENOME_ITEM,
461 {'name':k, 'value':unicode(v)})
462 mapped_reads = ElementTree.SubElement(lane, ElandLane.MAPPED_READS)
463 for k, v in self.mapped_reads.items():
464 item = ElementTree.SubElement(
465 mapped_reads, ElandLane.MAPPED_ITEM,
466 {'name':k, 'value':unicode(v)})
467 match_codes = ElementTree.SubElement(lane, ElandLane.MATCH_CODES)
468 for k, v in self.match_codes.items():
469 item = ElementTree.SubElement(
470 match_codes, ElandLane.MATCH_ITEM,
471 {'name':k, 'value':unicode(v)})
472 reads = ElementTree.SubElement(lane, ElandLane.READS)
473 reads.text = unicode(self.reads)
477 def set_elements(self, tree):
478 if tree.tag != ElandLane.LANE:
479 raise ValueError('Exptecting %s' % (ElandLane.LANE,))
481 tag = element.tag.lower()
482 if tag == ElandLane.GENOME_MAP.lower():
483 for child in element:
484 name = child.attrib['name']
485 value = child.attrib['value']
486 self.genome_map[name] = value
487 elif tag == ElandLane.MAPPED_READS.lower():
488 for child in element:
489 name = child.attrib['name']
490 value = child.attrib['value']
491 self._mapped_reads[name] = int(value)
492 elif tag == ElandLane.MATCH_CODES.lower():
493 for child in element:
494 name = child.attrib['name']
495 value = int(child.attrib['value'])
496 self._match_codes[name] = value
497 elif tag == ElandLane.READS.lower():
498 self._reads = int(element.text)
500 logging.warn("ElandLane unrecognized tag %s" % (element.tag,))
505 Summarize information from eland files
509 ELAND = 'ElandCollection'
513 def __init__(self, xml=None):
514 # we need information from the gerald config.xml
518 self.set_elements(xml)
521 return len(self.results)
524 return self.results.keys()
527 return self.results.values()
530 return self.results.items()
532 def __getitem__(self, key):
533 return self.results[key]
535 def get_elements(self):
536 root = ElementTree.Element(ELAND.ELAND,
537 {'version': unicode(ELAND.XML_VERSION)})
538 for lane_id, lane in self.results.items():
539 eland_lane = lane.get_elements()
540 eland_lane.attrib[ELAND.LANE_ID] = unicode(lane_id)
541 root.append(eland_lane)
544 def set_elements(self, tree):
545 if tree.tag.lower() != ELAND.ELAND.lower():
546 raise ValueError('Expecting %s', ELAND.ELAND)
547 for element in list(tree):
548 lane_id = element.attrib[ELAND.LANE_ID]
549 lane = ElandLane(xml=element)
550 self.results[lane_id] = lane
552 def eland(basedir, gerald=None, genome_maps=None):
554 for pathname in glob(os.path.join(basedir, "*_eland_result.txt")):
555 # extract the sample name
556 path, name = os.path.split(pathname)
557 split_name = name.split('_')
558 sample_name = split_name[0]
559 lane_id = split_name[1]
561 if genome_maps is not None:
562 genome_map = genome_maps[lane_id]
563 elif gerald is not None:
564 genome_dir = gerald.lanes[lane_id].eland_genome
565 genome_map = build_genome_fasta_map(genome_dir)
569 eland_result = ElandLane(pathname, genome_map)
570 e.results[lane_id] = eland_result