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
17 from gaworkflow.util.opener import autoopen
21 Capture meaning out of the GERALD directory
25 RUN_PARAMETERS='RunParameters'
28 class LaneParameters(object):
30 Make it easy to access elements of LaneSpecificRunParameters from python
32 def __init__(self, gerald, key):
36 def __get_attribute(self, xml_tag):
37 subtree = self._gerald.tree.find('LaneSpecificRunParameters')
38 container = subtree.find(xml_tag)
41 if len(container.getchildren()) != LANES_PER_FLOWCELL:
42 raise RuntimeError('GERALD config.xml file changed')
43 lanes = [x.tag.split('_')[1] for x in container.getchildren()]
44 index = lanes.index(self._key)
45 element = container[index]
47 def _get_analysis(self):
48 return self.__get_attribute('ANALYSIS')
49 analysis = property(_get_analysis)
51 def _get_eland_genome(self):
52 genome = self.__get_attribute('ELAND_GENOME')
53 # default to the chipwide parameters if there isn't an
54 # entry in the lane specific paramaters
56 subtree = self._gerald.tree.find('ChipWideRunParameters')
57 container = subtree.find('ELAND_GENOME')
58 genome = container.text
60 eland_genome = property(_get_eland_genome)
62 def _get_read_length(self):
63 return self.__get_attribute('READ_LENGTH')
64 read_length = property(_get_read_length)
66 def _get_use_bases(self):
67 return self.__get_attribute('USE_BASES')
68 use_bases = property(_get_use_bases)
70 class LaneSpecificRunParameters(object):
72 Provide access to LaneSpecificRunParameters
74 def __init__(self, gerald):
77 def __getitem__(self, key):
78 return Gerald.LaneParameters(self._gerald, key)
80 if self._keys is None:
81 tree = self._gerald.tree
82 analysis = tree.find('LaneSpecificRunParameters/ANALYSIS')
83 # according to the pipeline specs I think their fields
84 # are sampleName_laneID, with sampleName defaulting to s
85 # since laneIDs are constant lets just try using
87 self._keys = [ x.tag.split('_')[1] for x in analysis]
90 return [ self[x] for x in self.keys() ]
92 return zip(self.keys(), self.values())
94 return len(self.keys())
96 def __init__(self, xml=None):
100 # parse lane parameters out of the config.xml file
101 self.lanes = Gerald.LaneSpecificRunParameters(self)
104 self.eland_results = None
107 self.set_elements(xml)
110 if self.tree is None:
111 return datetime.today()
112 timestamp = self.tree.findtext('ChipWideRunParameters/TIME_STAMP')
113 epochstamp = time.mktime(time.strptime(timestamp, '%c'))
114 return datetime.fromtimestamp(epochstamp)
115 date = property(_get_date)
118 return time.mktime(self.date.timetuple())
119 time = property(_get_time, doc='return run time as seconds since epoch')
121 def _get_version(self):
122 if self.tree is None:
124 return self.tree.findtext('ChipWideRunParameters/SOFTWARE_VERSION')
125 version = property(_get_version)
129 Debugging function, report current object
131 print 'Gerald version:', self.version
132 print 'Gerald run date:', self.date
133 print 'Gerald config.xml:', self.tree
136 def get_elements(self):
137 if self.tree is None or self.summary is None:
140 gerald = ElementTree.Element(Gerald.GERALD,
141 {'version': unicode(Gerald.XML_VERSION)})
142 gerald.append(self.tree)
143 gerald.append(self.summary.get_elements())
144 if self.eland_results:
145 gerald.append(self.eland_results.get_elements())
148 def set_elements(self, tree):
149 if tree.tag != Gerald.GERALD:
150 raise ValueError('exptected GERALD')
151 xml_version = int(tree.attrib.get('version', 0))
152 if xml_version > Gerald.XML_VERSION:
153 logging.warn('XML tree is a higher version than this class')
154 for element in list(tree):
155 tag = element.tag.lower()
156 if tag == Gerald.RUN_PARAMETERS.lower():
158 elif tag == Gerald.SUMMARY.lower():
159 self.summary = Summary(xml=element)
160 elif tag == ELAND.ELAND.lower():
161 self.eland_results = ELAND(xml=element)
163 logging.warn("Unrecognized tag %s" % (element.tag,))
166 def gerald(pathname):
168 g.pathname = pathname
169 path, name = os.path.split(pathname)
170 config_pathname = os.path.join(pathname, 'config.xml')
171 g.tree = ElementTree.parse(config_pathname).getroot()
173 # parse Summary.htm file
174 summary_pathname = os.path.join(pathname, 'Summary.htm')
175 g.summary = Summary(summary_pathname)
177 g.eland_results = eland(g.pathname, g)
182 Convert a value to int if its an int otherwise a float.
186 except ValueError, e:
190 def parse_mean_range(value):
192 Parse values like 123 +/- 4.5
194 if value.strip() == 'unknown':
197 average, pm, deviation = value.split()
199 raise RuntimeError("Summary.htm file format changed")
200 return tonumber(average), tonumber(deviation)
202 def make_mean_range_element(parent, name, mean, deviation):
204 Make an ElementTree subelement <Name mean='mean', deviation='deviation'/>
206 element = ElementTree.SubElement(parent, name,
207 { 'mean': unicode(mean),
208 'deviation': unicode(deviation)})
211 def parse_mean_range_element(element):
213 Grab mean/deviation out of element
215 return (tonumber(element.attrib['mean']),
216 tonumber(element.attrib['deviation']))
218 class Summary(object):
220 Extract some useful information from the Summary.htm file
225 class LaneResultSummary(object):
227 Parse the LaneResultSummary table out of Summary.htm
228 Mostly for the cluster number
230 LANE_RESULT_SUMMARY = 'LaneResultSummary'
232 'Cluster': 'cluster',
233 'AverageFirstCycleIntensity': 'average_first_cycle_intensity',
234 'PercentIntensityAfter20Cycles': 'percent_intensity_after_20_cycles',
235 'PercentPassFilterClusters': 'percent_pass_filter_clusters',
236 'PercentPassFilterAlign': 'percent_pass_filter_align',
237 'AverageAlignmentScore': 'average_alignment_score',
238 'PercentErrorRate': 'percent_error_rate'
241 def __init__(self, html=None, xml=None):
244 self.average_first_cycle_intensity = None
245 self.percent_intensity_after_20_cycles = None
246 self.percent_pass_filter_clusters = None
247 self.percent_pass_filter_align = None
248 self.average_alignment_score = None
249 self.percent_error_rate = None
252 self.set_elements_from_html(html)
254 self.set_elements(xml)
256 def set_elements_from_html(self, row_element):
257 data = [ flatten(x) for x in row_element ]
259 raise RuntimeError("Summary.htm file format changed")
262 self.cluster = parse_mean_range(data[1])
263 self.average_first_cycle_intensity = parse_mean_range(data[2])
264 self.percent_intensity_after_20_cycles = parse_mean_range(data[3])
265 self.percent_pass_filter_clusters = parse_mean_range(data[4])
266 self.percent_pass_filter_align = parse_mean_range(data[5])
267 self.average_alignment_score = parse_mean_range(data[6])
268 self.percent_error_rate = parse_mean_range(data[7])
270 def get_elements(self):
271 lane_result = ElementTree.Element(
272 Summary.LaneResultSummary.LANE_RESULT_SUMMARY,
274 for tag, variable_name in Summary.LaneResultSummary.TAGS.items():
275 element = make_mean_range_element(
278 *getattr(self, variable_name)
282 def set_elements(self, tree):
283 if tree.tag != Summary.LaneResultSummary.LANE_RESULT_SUMMARY:
284 raise ValueError('Expected %s' % (
285 Summary.LaneResultSummary.LANE_RESULT_SUMMARY))
286 self.lane = tree.attrib['lane']
287 tags = Summary.LaneResultSummary.TAGS
288 for element in list(tree):
290 variable_name = tags[element.tag]
291 setattr(self, variable_name,
292 parse_mean_range_element(element))
294 logging.warn('Unrecognized tag %s' % (element.tag,))
296 def __init__(self, filename=None, xml=None):
297 self.lane_results = {}
299 if filename is not None:
300 self._extract_lane_results(filename)
302 self.set_elements(xml)
304 def __getitem__(self, key):
305 return self.lane_results[key]
308 return len(self.lane_results)
311 return self.lane_results.keys()
314 return self.lane_results.values()
317 return self.lane_results.items()
319 def _extract_lane_results(self, pathname):
321 extract the Lane Results Summary table
323 tree = ElementTree.parse(pathname).getroot()
324 if flatten(tree.findall('*//h2')[3]) != 'Lane Results Summary':
325 raise RuntimeError("Summary.htm file format changed")
327 tables = tree.findall('*//table')
329 # parse lane result summary
330 lane_summary = tables[2]
331 rows = lane_summary.getchildren()
332 headers = rows[0].getchildren()
333 if flatten(headers[2]) != 'Av 1st Cycle Int ':
334 raise RuntimeError("Summary.htm file format changed")
337 lrs = Summary.LaneResultSummary(html=r)
338 self.lane_results[lrs.lane] = lrs
340 def get_elements(self):
341 summary = ElementTree.Element(Summary.SUMMARY,
342 {'version': unicode(Summary.XML_VERSION)})
343 for lane in self.lane_results.values():
344 summary.append(lane.get_elements())
347 def set_elements(self, tree):
348 if tree.tag != Summary.SUMMARY:
349 return ValueError("Expected %s" % (Summary.SUMMARY,))
350 xml_version = int(tree.attrib.get('version', 0))
351 if xml_version > Summary.XML_VERSION:
352 logging.warn('Summary XML tree is a higher version than this class')
353 for element in list(tree):
354 lrs = Summary.LaneResultSummary()
355 lrs.set_elements(element)
356 self.lane_results[lrs.lane] = lrs
360 Debugging function, report current object
365 def build_genome_fasta_map(genome_dir):
366 # build fasta to fasta file map
367 genome = genome_dir.split(os.path.sep)[-1]
369 for vld_file in glob(os.path.join(genome_dir, '*.vld')):
371 if os.path.islink(vld_file):
373 vld_file = os.path.realpath(vld_file)
374 path, vld_name = os.path.split(vld_file)
375 name, ext = os.path.splitext(vld_name)
377 fasta_map[name] = name
379 fasta_map[name] = os.path.join(genome, name)
382 class ElandLane(object):
384 Process an eland result file
388 SAMPLE_NAME = 'SampleName'
390 GENOME_MAP = 'GenomeMap'
391 GENOME_ITEM = 'GenomeItem'
392 MAPPED_READS = 'MappedReads'
393 MAPPED_ITEM = 'MappedItem'
394 MATCH_CODES = 'MatchCodes'
398 def __init__(self, pathname=None, genome_map=None, xml=None):
399 self.pathname = pathname
400 self._sample_name = None
403 self._mapped_reads = None
404 self._match_codes = None
405 if genome_map is None:
407 self.genome_map = genome_map
410 self.set_elements(xml)
414 Actually read the file and actually count the reads
416 # can't do anything if we don't have a file to process
417 if self.pathname is None:
420 if os.stat(self.pathname)[stat.ST_SIZE] == 0:
421 raise RuntimeError("Eland isn't done, try again later.")
426 match_codes = {'NM':0, 'QC':0, 'RM':0,
427 'U0':0, 'U1':0, 'U2':0,
428 'R0':0, 'R1':0, 'R2':0,
430 for line in autoopen(self.pathname,'r'):
432 fields = line.split()
434 # match_codes[code] = match_codes.setdefault(code, 0) + 1
435 # the QC/NM etc codes are in the 3rd field and always present
436 match_codes[fields[2]] += 1
437 # ignore lines that don't have a fasta filename
440 fasta = self.genome_map.get(fields[6], fields[6])
441 mapped_reads[fasta] = mapped_reads.setdefault(fasta, 0) + 1
442 self._match_codes = match_codes
443 self._mapped_reads = mapped_reads
446 def _update_name(self):
447 # extract the sample name
448 if self.pathname is None:
451 path, name = os.path.split(self.pathname)
452 split_name = name.split('_')
453 self._sample_name = split_name[0]
454 self._lane_id = split_name[1]
456 def _get_sample_name(self):
457 if self._sample_name is None:
459 return self._sample_name
460 sample_name = property(_get_sample_name)
462 def _get_lane_id(self):
463 if self._lane_id is None:
466 lane_id = property(_get_lane_id)
468 def _get_reads(self):
469 if self._reads is None:
472 reads = property(_get_reads)
474 def _get_mapped_reads(self):
475 if self._mapped_reads is None:
477 return self._mapped_reads
478 mapped_reads = property(_get_mapped_reads)
480 def _get_match_codes(self):
481 if self._match_codes is None:
483 return self._match_codes
484 match_codes = property(_get_match_codes)
486 def get_elements(self):
487 lane = ElementTree.Element(ElandLane.LANE,
489 unicode(ElandLane.XML_VERSION)})
490 sample_tag = ElementTree.SubElement(lane, ElandLane.SAMPLE_NAME)
491 sample_tag.text = self.sample_name
492 lane_tag = ElementTree.SubElement(lane, ElandLane.LANE_ID)
493 lane_tag.text = self.lane_id
494 genome_map = ElementTree.SubElement(lane, ElandLane.GENOME_MAP)
495 for k, v in self.genome_map.items():
496 item = ElementTree.SubElement(
497 genome_map, ElandLane.GENOME_ITEM,
498 {'name':k, 'value':unicode(v)})
499 mapped_reads = ElementTree.SubElement(lane, ElandLane.MAPPED_READS)
500 for k, v in self.mapped_reads.items():
501 item = ElementTree.SubElement(
502 mapped_reads, ElandLane.MAPPED_ITEM,
503 {'name':k, 'value':unicode(v)})
504 match_codes = ElementTree.SubElement(lane, ElandLane.MATCH_CODES)
505 for k, v in self.match_codes.items():
506 item = ElementTree.SubElement(
507 match_codes, ElandLane.MATCH_ITEM,
508 {'name':k, 'value':unicode(v)})
509 reads = ElementTree.SubElement(lane, ElandLane.READS)
510 reads.text = unicode(self.reads)
514 def set_elements(self, tree):
515 if tree.tag != ElandLane.LANE:
516 raise ValueError('Exptecting %s' % (ElandLane.LANE,))
519 self._mapped_reads = {}
520 self._match_codes = {}
523 tag = element.tag.lower()
524 if tag == ElandLane.SAMPLE_NAME.lower():
525 self._sample_name = element.text
526 elif tag == ElandLane.LANE_ID.lower():
527 self._lane_id = element.text
528 elif tag == ElandLane.GENOME_MAP.lower():
529 for child in element:
530 name = child.attrib['name']
531 value = child.attrib['value']
532 self.genome_map[name] = value
533 elif tag == ElandLane.MAPPED_READS.lower():
534 for child in element:
535 name = child.attrib['name']
536 value = child.attrib['value']
537 self._mapped_reads[name] = int(value)
538 elif tag == ElandLane.MATCH_CODES.lower():
539 for child in element:
540 name = child.attrib['name']
541 value = int(child.attrib['value'])
542 self._match_codes[name] = value
543 elif tag == ElandLane.READS.lower():
544 self._reads = int(element.text)
546 logging.warn("ElandLane unrecognized tag %s" % (element.tag,))
548 def extract_eland_sequence(instream, outstream, start, end):
550 Extract a chunk of sequence out of an eland file
552 for line in instream:
553 record = line.split()
555 result = [record[0], record[1][start:end]]
557 result = [record[0][start:end]]
558 outstream.write("\t".join(result))
559 outstream.write(os.linesep)
563 Summarize information from eland files
567 ELAND = 'ElandCollection'
571 def __init__(self, xml=None):
572 # we need information from the gerald config.xml
576 self.set_elements(xml)
579 return len(self.results)
582 return self.results.keys()
585 return self.results.values()
588 return self.results.items()
590 def __getitem__(self, key):
591 return self.results[key]
593 def get_elements(self):
594 root = ElementTree.Element(ELAND.ELAND,
595 {'version': unicode(ELAND.XML_VERSION)})
596 for lane_id, lane in self.results.items():
597 eland_lane = lane.get_elements()
598 eland_lane.attrib[ELAND.LANE_ID] = unicode(lane_id)
599 root.append(eland_lane)
602 def set_elements(self, tree):
603 if tree.tag.lower() != ELAND.ELAND.lower():
604 raise ValueError('Expecting %s', ELAND.ELAND)
605 for element in list(tree):
606 lane_id = element.attrib[ELAND.LANE_ID]
607 lane = ElandLane(xml=element)
608 self.results[lane_id] = lane
610 def eland(basedir, gerald=None, genome_maps=None):
613 file_list = glob(os.path.join(basedir, "*_eland_result.txt"))
614 if len(file_list) == 0:
615 # lets handle compressed eland files too
616 file_list = glob(os.path.join(basedir, "*_eland_result.txt.bz2"))
618 for pathname in file_list:
619 # yes the lane_id is also being computed in ElandLane._update
620 # I didn't want to clutter up my constructor
621 # but I needed to persist the sample_name/lane_id for
622 # runfolder summary_report
623 path, name = os.path.split(pathname)
624 split_name = name.split('_')
625 lane_id = split_name[1]
627 if genome_maps is not None:
628 genome_map = genome_maps[lane_id]
629 elif gerald is not None:
630 genome_dir = gerald.lanes[lane_id].eland_genome
631 genome_map = build_genome_fasta_map(genome_dir)
635 eland_result = ElandLane(pathname, genome_map)
636 e.results[lane_id] = eland_result