gaworkflow/pipeline/gerald.py

   1 """
   2 Provide access to information stored in the GERALD directory.
   3 """
   4 from datetime import datetime, date
   5 from glob import glob
   6 import logging
   7 import os
   8 import stat
   9 import time
  10 import types
  11
  12 from gaworkflow.pipeline.runfolder import \
  13    ElementTree, \
  14    EUROPEAN_STRPTIME, \
  15    LANES_PER_FLOWCELL, \
  16    VERSION_RE
  17 from gaworkflow.util.ethelp import indent, flatten
  18 from gaworkflow.util.opener import autoopen
  19
  20 class Gerald(object):
  21     """
  22     Capture meaning out of the GERALD directory
  23     """
  24     XML_VERSION = 1
  25     GERALD='Gerald'
  26     RUN_PARAMETERS='RunParameters'
  27     SUMMARY='Summary'
  28
  29     class LaneParameters(object):
  30         """
  31         Make it easy to access elements of LaneSpecificRunParameters from python
  32         """
  33         def __init__(self, gerald, key):
  34             self._gerald = gerald
  35             self._key = key
  36
  37         def __get_attribute(self, xml_tag):
  38             subtree = self._gerald.tree.find('LaneSpecificRunParameters')
  39             container = subtree.find(xml_tag)
  40             if container is None:
  41                 return None
  42             if len(container.getchildren()) > LANES_PER_FLOWCELL:
  43                 raise RuntimeError('GERALD config.xml file changed')
  44             lanes = [x.tag.split('_')[1] for x in container.getchildren()]
  45             index = lanes.index(self._key)
  46             element = container[index]
  47             return element.text
  48         def _get_analysis(self):
  49             return self.__get_attribute('ANALYSIS')
  50         analysis = property(_get_analysis)
  51
  52         def _get_eland_genome(self):
  53             genome = self.__get_attribute('ELAND_GENOME')
  54             # default to the chipwide parameters if there isn't an
  55             # entry in the lane specific paramaters
  56             if genome is None:
  57                 subtree = self._gerald.tree.find('ChipWideRunParameters')
  58                 container = subtree.find('ELAND_GENOME')
  59                 genome = container.text
  60             return genome
  61         eland_genome = property(_get_eland_genome)
  62
  63         def _get_read_length(self):
  64             return self.__get_attribute('READ_LENGTH')
  65         read_length = property(_get_read_length)
  66
  67         def _get_use_bases(self):
  68             return self.__get_attribute('USE_BASES')
  69         use_bases = property(_get_use_bases)
  70
  71     class LaneSpecificRunParameters(object):
  72         """
  73         Provide access to LaneSpecificRunParameters
  74         """
  75         def __init__(self, gerald):
  76             self._gerald = gerald
  77             self._keys = None
  78         def __getitem__(self, key):
  79             return Gerald.LaneParameters(self._gerald, key)
  80         def keys(self):
  81             if self._keys is None:
  82                 tree = self._gerald.tree
  83                 analysis = tree.find('LaneSpecificRunParameters/ANALYSIS')
  84                 # according to the pipeline specs I think their fields
  85                 # are sampleName_laneID, with sampleName defaulting to s
  86                 # since laneIDs are constant lets just try using
  87                 # those consistently.
  88                 self._keys = [ x.tag.split('_')[1] for x in analysis]
  89             return self._keys
  90         def values(self):
  91             return [ self[x] for x in self.keys() ]
  92         def items(self):
  93             return zip(self.keys(), self.values())
  94         def __len__(self):
  95             return len(self.keys())
  96
  97     def __init__(self, xml=None):
  98         self.pathname = None
  99         self.tree = None
 100
 101         # parse lane parameters out of the config.xml file
 102         self.lanes = Gerald.LaneSpecificRunParameters(self)
 103
 104         self.summary = None
 105         self.eland_results = None
 106
 107         if xml is not None:
 108             self.set_elements(xml)
 109
 110     def _get_date(self):
 111         if self.tree is None:
 112             return datetime.today()
 113         timestamp = self.tree.findtext('ChipWideRunParameters/TIME_STAMP')
 114         epochstamp = time.mktime(time.strptime(timestamp, '%c'))
 115         return datetime.fromtimestamp(epochstamp)
 116     date = property(_get_date)
 117
 118     def _get_time(self):
 119         return time.mktime(self.date.timetuple())
 120     time = property(_get_time, doc='return run time as seconds since epoch')
 121
 122     def _get_version(self):
 123         if self.tree is None:
 124             return None
 125         return self.tree.findtext('ChipWideRunParameters/SOFTWARE_VERSION')
 126     version = property(_get_version)
 127
 128     def dump(self):
 129         """
 130         Debugging function, report current object
 131         """
 132         print 'Gerald version:', self.version
 133         print 'Gerald run date:', self.date
 134         print 'Gerald config.xml:', self.tree
 135         self.summary.dump()
 136
 137     def get_elements(self):
 138         if self.tree is None or self.summary is None:
 139             return None
 140
 141         gerald = ElementTree.Element(Gerald.GERALD,
 142                                      {'version': unicode(Gerald.XML_VERSION)})
 143         gerald.append(self.tree)
 144         gerald.append(self.summary.get_elements())
 145         if self.eland_results:
 146             gerald.append(self.eland_results.get_elements())
 147         return gerald
 148
 149     def set_elements(self, tree):
 150         if tree.tag !=  Gerald.GERALD:
 151             raise ValueError('exptected GERALD')
 152         xml_version = int(tree.attrib.get('version', 0))
 153         if xml_version > Gerald.XML_VERSION:
 154             logging.warn('XML tree is a higher version than this class')
 155         for element in list(tree):
 156             tag = element.tag.lower()
 157             if tag == Gerald.RUN_PARAMETERS.lower():
 158                 self.tree = element
 159             elif tag == Gerald.SUMMARY.lower():
 160                 self.summary = Summary(xml=element)
 161             elif tag == ELAND.ELAND.lower():
 162                 self.eland_results = ELAND(xml=element)
 163             else:
 164                 logging.warn("Unrecognized tag %s" % (element.tag,))
 165
 166
 167 def gerald(pathname):
 168     g = Gerald()
 169     g.pathname = pathname
 170     path, name = os.path.split(pathname)
 171     config_pathname = os.path.join(pathname, 'config.xml')
 172     g.tree = ElementTree.parse(config_pathname).getroot()
 173
 174     # parse Summary.htm file
 175     summary_pathname = os.path.join(pathname, 'Summary.htm')
 176     g.summary = Summary(summary_pathname)
 177     # parse eland files
 178     g.eland_results = eland(g.pathname, g)
 179     return g
 180
 181 def tonumber(v):
 182     """
 183     Convert a value to int if its an int otherwise a float.
 184     """
 185     try:
 186         v = int(v)
 187     except ValueError, e:
 188         v = float(v)
 189     return v
 190
 191 def parse_mean_range(value):
 192     """
 193     Parse values like 123 +/- 4.5
 194     """
 195     if value.strip() == 'unknown':
 196         return 0, 0
 197
 198     average, pm, deviation = value.split()
 199     if pm != '+/-':
 200         raise RuntimeError("Summary.htm file format changed")
 201     return tonumber(average), tonumber(deviation)
 202
 203 def make_mean_range_element(parent, name, mean, deviation):
 204     """
 205     Make an ElementTree subelement <Name mean='mean', deviation='deviation'/>
 206     """
 207     element = ElementTree.SubElement(parent, name,
 208                                      { 'mean': unicode(mean),
 209                                        'deviation': unicode(deviation)})
 210     return element
 211
 212 def parse_mean_range_element(element):
 213     """
 214     Grab mean/deviation out of element
 215     """
 216     return (tonumber(element.attrib['mean']),
 217             tonumber(element.attrib['deviation']))
 218
 219 def parse_summary_element(element):
 220     """
 221     Determine if we have a simple element or a mean/deviation element
 222     """
 223     if len(element.attrib) > 0:
 224         return parse_mean_range_element(element)
 225     else:
 226         return element.text
 227
 228 class Summary(object):
 229     """
 230     Extract some useful information from the Summary.htm file
 231     """
 232     XML_VERSION = 2
 233     SUMMARY = 'Summary'
 234
 235     class LaneResultSummary(object):
 236         """
 237         Parse the LaneResultSummary table out of Summary.htm
 238         Mostly for the cluster number
 239         """
 240         LANE_RESULT_SUMMARY = 'LaneResultSummary'
 241         TAGS = {
 242           'LaneYield': 'lane_yield',
 243           'Cluster': 'cluster', # Raw
 244           'ClusterPF': 'cluster_pass_filter',
 245           'AverageFirstCycleIntensity': 'average_first_cycle_intensity',
 246           'PercentIntensityAfter20Cycles': 'percent_intensity_after_20_cycles',
 247           'PercentPassFilterClusters': 'percent_pass_filter_clusters',
 248           'PercentPassFilterAlign': 'percent_pass_filter_align',
 249           'AverageAlignmentScore': 'average_alignment_score',
 250           'PercentErrorRate': 'percent_error_rate'
 251         }
 252
 253         def __init__(self, html=None, xml=None):
 254             self.lane = None
 255             self.lane_yield = None
 256             self.cluster = None
 257             self.cluster_pass_filter = None
 258             self.average_first_cycle_intensity = None
 259             self.percent_intensity_after_20_cycles = None
 260             self.percent_pass_filter_clusters = None
 261             self.percent_pass_filter_align = None
 262             self.average_alignment_score = None
 263             self.percent_error_rate = None
 264
 265             if html is not None:
 266                 self.set_elements_from_html(html)
 267             if xml is not None:
 268                 self.set_elements(xml)
 269
 270         def set_elements_from_html(self, data):
 271             if not len(data) in (8,10):
 272                 raise RuntimeError("Summary.htm file format changed")
 273
 274             # same in pre-0.3.0 Summary file and 0.3 summary file
 275             self.lane = data[0]
 276
 277             if len(data) == 8:
 278                 parsed_data = [ parse_mean_range(x) for x in data[1:] ]
 279                 # this is the < 0.3 Pipeline version
 280                 self.cluster = parsed_data[0]
 281                 self.average_first_cycle_intensity = parsed_data[1]
 282                 self.percent_intensity_after_20_cycles = parsed_data[2]
 283                 self.percent_pass_filter_clusters = parsed_data[3]
 284                 self.percent_pass_filter_align = parsed_data[4]
 285                 self.average_alignment_score = parsed_data[5]
 286                 self.percent_error_rate = parsed_data[6]
 287             elif len(data) == 10:
 288                 parsed_data = [ parse_mean_range(x) for x in data[2:] ]
 289                 # this is the >= 0.3 summary file
 290                 self.lane_yield = data[1]
 291                 self.cluster = parsed_data[0]
 292                 self.cluster_pass_filter = parsed_data[1]
 293                 self.average_first_cycle_intensity = parsed_data[2]
 294                 self.percent_intensity_after_20_cycles = parsed_data[3]
 295                 self.percent_pass_filter_clusters = parsed_data[4]
 296                 self.percent_pass_filter_align = parsed_data[5]
 297                 self.average_alignment_score = parsed_data[6]
 298                 self.percent_error_rate = parsed_data[7]
 299
 300         def get_elements(self):
 301             lane_result = ElementTree.Element(
 302                             Summary.LaneResultSummary.LANE_RESULT_SUMMARY,
 303                             {'lane': self.lane})
 304             for tag, variable_name in Summary.LaneResultSummary.TAGS.items():
 305                 value = getattr(self, variable_name)
 306                 if value is None:
 307                     continue
 308                 # it looks like a sequence
 309                 elif type(value) in (types.TupleType, types.ListType):
 310                     element = make_mean_range_element(
 311                       lane_result,
 312                       tag,
 313                       *value
 314                     )
 315                 else:
 316                     element = ElementTree.SubElement(lane_result, tag)
 317                     element.text = value
 318             return lane_result
 319
 320         def set_elements(self, tree):
 321             if tree.tag != Summary.LaneResultSummary.LANE_RESULT_SUMMARY:
 322                 raise ValueError('Expected %s' % (
 323                         Summary.LaneResultSummary.LANE_RESULT_SUMMARY))
 324             self.lane = tree.attrib['lane']
 325             tags = Summary.LaneResultSummary.TAGS
 326             for element in list(tree):
 327                 try:
 328                     variable_name = tags[element.tag]
 329                     setattr(self, variable_name,
 330                             parse_summary_element(element))
 331                 except KeyError, e:
 332                     logging.warn('Unrecognized tag %s' % (element.tag,))
 333
 334     def __init__(self, filename=None, xml=None):
 335         self.lane_results = {}
 336
 337         if filename is not None:
 338             self._extract_lane_results(filename)
 339         if xml is not None:
 340             self.set_elements(xml)
 341
 342     def __getitem__(self, key):
 343         return self.lane_results[key]
 344
 345     def __len__(self):
 346         return len(self.lane_results)
 347
 348     def keys(self):
 349         return self.lane_results.keys()
 350
 351     def values(self):
 352         return self.lane_results.values()
 353
 354     def items(self):
 355         return self.lane_results.items()
 356
 357     def _flattened_row(self, row):
 358         """
 359         flatten the children of a <tr>...</tr>
 360         """
 361         return [flatten(x) for x in row.getchildren() ]
 362
 363     def _parse_table(self, table):
 364         """
 365         assumes the first line is the header of a table,
 366         and that the remaining rows are data
 367         """
 368         rows = table.getchildren()
 369         data = []
 370         for r in rows:
 371             data.append(self._flattened_row(r))
 372         return data
 373
 374     def _extract_named_tables(self, pathname):
 375         """
 376         extract all the 'named' tables from a Summary.htm file
 377         and return as a dictionary
 378
 379         Named tables are <h2>...</h2><table>...</table> pairs
 380         The contents of the h2 tag is considered to the name
 381         of the table.
 382         """
 383         tree = ElementTree.parse(pathname).getroot()
 384         body = tree.find('body')
 385         tables = {}
 386         for i in range(len(body)):
 387             if body[i].tag == 'h2' and body[i+1].tag == 'table':
 388                 # we have an interesting table
 389                 name = flatten(body[i])
 390                 table = body[i+1]
 391                 data = self._parse_table(table)
 392                 tables[name] = data
 393         return tables
 394
 395     def _extract_lane_results(self, pathname):
 396         """
 397         extract the Lane Results Summary table
 398         """
 399
 400         tables = self._extract_named_tables(pathname)
 401
 402         # parse lane result summary
 403         lane_summary = tables['Lane Results Summary']
 404         # this is version 1 of the summary file
 405         if len(lane_summary[-1]) == 8:
 406             # strip header
 407             headers = lane_summary[0]
 408             # grab the lane by lane data
 409             lane_summary = lane_summary[1:]
 410
 411         # this is version 2 of the summary file
 412         if len(lane_summary[-1]) == 10:
 413             # lane_summary[0] is a different less specific header row
 414             headers = lane_summary[1]
 415             lane_summary = lane_summary[2:10]
 416             # after the last lane, there's a set of chip wide averages
 417
 418         for r in lane_summary:
 419             lrs = Summary.LaneResultSummary(html=r)
 420             self.lane_results[lrs.lane] = lrs
 421
 422     def get_elements(self):
 423         summary = ElementTree.Element(Summary.SUMMARY,
 424                                       {'version': unicode(Summary.XML_VERSION)})
 425         for lane in self.lane_results.values():
 426             summary.append(lane.get_elements())
 427         return summary
 428
 429     def set_elements(self, tree):
 430         if tree.tag != Summary.SUMMARY:
 431             return ValueError("Expected %s" % (Summary.SUMMARY,))
 432         xml_version = int(tree.attrib.get('version', 0))
 433         if xml_version > Summary.XML_VERSION:
 434             logging.warn('Summary XML tree is a higher version than this class')
 435         for element in list(tree):
 436             lrs = Summary.LaneResultSummary()
 437             lrs.set_elements(element)
 438             self.lane_results[lrs.lane] = lrs
 439
 440     def dump(self):
 441         """
 442         Debugging function, report current object
 443         """
 444         pass
 445
 446
 447 def build_genome_fasta_map(genome_dir):
 448     # build fasta to fasta file map
 449     genome = genome_dir.split(os.path.sep)[-1]
 450     fasta_map = {}
 451     for vld_file in glob(os.path.join(genome_dir, '*.vld')):
 452         is_link = False
 453         if os.path.islink(vld_file):
 454             is_link = True
 455         vld_file = os.path.realpath(vld_file)
 456         path, vld_name = os.path.split(vld_file)
 457         name, ext = os.path.splitext(vld_name)
 458         if is_link:
 459             fasta_map[name] = name
 460         else:
 461             fasta_map[name] = os.path.join(genome, name)
 462     return fasta_map
 463
 464 class ElandLane(object):
 465     """
 466     Process an eland result file
 467     """
 468     XML_VERSION = 1
 469     LANE = 'ElandLane'
 470     SAMPLE_NAME = 'SampleName'
 471     LANE_ID = 'LaneID'
 472     GENOME_MAP = 'GenomeMap'
 473     GENOME_ITEM = 'GenomeItem'
 474     MAPPED_READS = 'MappedReads'
 475     MAPPED_ITEM = 'MappedItem'
 476     MATCH_CODES = 'MatchCodes'
 477     MATCH_ITEM = 'Code'
 478     READS = 'Reads'
 479
 480     def __init__(self, pathname=None, genome_map=None, xml=None):
 481         self.pathname = pathname
 482         self._sample_name = None
 483         self._lane_id = None
 484         self._reads = None
 485         self._mapped_reads = None
 486         self._match_codes = None
 487         if genome_map is None:
 488             genome_map = {}
 489         self.genome_map = genome_map
 490
 491         if xml is not None:
 492             self.set_elements(xml)
 493
 494     def _update(self):
 495         """
 496         Actually read the file and actually count the reads
 497         """
 498         # can't do anything if we don't have a file to process
 499         if self.pathname is None:
 500             return
 501
 502         if os.stat(self.pathname)[stat.ST_SIZE] == 0:
 503             raise RuntimeError("Eland isn't done, try again later.")
 504
 505         reads = 0
 506         mapped_reads = {}
 507
 508         match_codes = {'NM':0, 'QC':0, 'RM':0,
 509                        'U0':0, 'U1':0, 'U2':0,
 510                        'R0':0, 'R1':0, 'R2':0,
 511                       }
 512         for line in autoopen(self.pathname,'r'):
 513             reads += 1
 514             fields = line.split()
 515             # code = fields[2]
 516             # match_codes[code] = match_codes.setdefault(code, 0) + 1
 517             # the QC/NM etc codes are in the 3rd field and always present
 518             match_codes[fields[2]] += 1
 519             # ignore lines that don't have a fasta filename
 520             if len(fields) < 7:
 521                 continue
 522             fasta = self.genome_map.get(fields[6], fields[6])
 523             mapped_reads[fasta] = mapped_reads.setdefault(fasta, 0) + 1
 524         self._match_codes = match_codes
 525         self._mapped_reads = mapped_reads
 526         self._reads = reads
 527
 528     def _update_name(self):
 529         # extract the sample name
 530         if self.pathname is None:
 531             return
 532
 533         path, name = os.path.split(self.pathname)
 534         split_name = name.split('_')
 535         self._sample_name = split_name[0]
 536         self._lane_id = split_name[1]
 537
 538     def _get_sample_name(self):
 539         if self._sample_name is None:
 540             self._update_name()
 541         return self._sample_name
 542     sample_name = property(_get_sample_name)
 543
 544     def _get_lane_id(self):
 545         if self._lane_id is None:
 546             self._update_name()
 547         return self._lane_id
 548     lane_id = property(_get_lane_id)
 549
 550     def _get_reads(self):
 551         if self._reads is None:
 552             self._update()
 553         return self._reads
 554     reads = property(_get_reads)
 555
 556     def _get_mapped_reads(self):
 557         if self._mapped_reads is None:
 558             self._update()
 559         return self._mapped_reads
 560     mapped_reads = property(_get_mapped_reads)
 561
 562     def _get_match_codes(self):
 563         if self._match_codes is None:
 564             self._update()
 565         return self._match_codes
 566     match_codes = property(_get_match_codes)
 567
 568     def get_elements(self):
 569         lane = ElementTree.Element(ElandLane.LANE,
 570                                    {'version':
 571                                     unicode(ElandLane.XML_VERSION)})
 572         sample_tag = ElementTree.SubElement(lane, ElandLane.SAMPLE_NAME)
 573         sample_tag.text = self.sample_name
 574         lane_tag = ElementTree.SubElement(lane, ElandLane.LANE_ID)
 575         lane_tag.text = self.lane_id
 576         genome_map = ElementTree.SubElement(lane, ElandLane.GENOME_MAP)
 577         for k, v in self.genome_map.items():
 578             item = ElementTree.SubElement(
 579                 genome_map, ElandLane.GENOME_ITEM,
 580                 {'name':k, 'value':unicode(v)})
 581         mapped_reads = ElementTree.SubElement(lane, ElandLane.MAPPED_READS)
 582         for k, v in self.mapped_reads.items():
 583             item = ElementTree.SubElement(
 584                 mapped_reads, ElandLane.MAPPED_ITEM,
 585                 {'name':k, 'value':unicode(v)})
 586         match_codes = ElementTree.SubElement(lane, ElandLane.MATCH_CODES)
 587         for k, v in self.match_codes.items():
 588             item = ElementTree.SubElement(
 589                 match_codes, ElandLane.MATCH_ITEM,
 590                 {'name':k, 'value':unicode(v)})
 591         reads = ElementTree.SubElement(lane, ElandLane.READS)
 592         reads.text = unicode(self.reads)
 593
 594         return lane
 595
 596     def set_elements(self, tree):
 597         if tree.tag != ElandLane.LANE:
 598             raise ValueError('Exptecting %s' % (ElandLane.LANE,))
 599
 600         # reset dictionaries
 601         self._mapped_reads = {}
 602         self._match_codes = {}
 603
 604         for element in tree:
 605             tag = element.tag.lower()
 606             if tag == ElandLane.SAMPLE_NAME.lower():
 607                 self._sample_name = element.text
 608             elif tag == ElandLane.LANE_ID.lower():
 609                 self._lane_id = element.text
 610             elif tag == ElandLane.GENOME_MAP.lower():
 611                 for child in element:
 612                     name = child.attrib['name']
 613                     value = child.attrib['value']
 614                     self.genome_map[name] = value
 615             elif tag == ElandLane.MAPPED_READS.lower():
 616                 for child in element:
 617                     name = child.attrib['name']
 618                     value = child.attrib['value']
 619                     self._mapped_reads[name] = int(value)
 620             elif tag == ElandLane.MATCH_CODES.lower():
 621                 for child in element:
 622                     name = child.attrib['name']
 623                     value = int(child.attrib['value'])
 624                     self._match_codes[name] = value
 625             elif tag == ElandLane.READS.lower():
 626                 self._reads = int(element.text)
 627             else:
 628                 logging.warn("ElandLane unrecognized tag %s" % (element.tag,))
 629
 630 def extract_eland_sequence(instream, outstream, start, end):
 631     """
 632     Extract a chunk of sequence out of an eland file
 633     """
 634     for line in instream:
 635         record = line.split()
 636         if len(record) > 1:
 637             result = [record[0], record[1][start:end]]
 638         else:
 639             result = [record[0][start:end]]
 640         outstream.write("\t".join(result))
 641         outstream.write(os.linesep)
 642
 643 class ELAND(object):
 644     """
 645     Summarize information from eland files
 646     """
 647     XML_VERSION = 1
 648
 649     ELAND = 'ElandCollection'
 650     LANE = 'Lane'
 651     LANE_ID = 'id'
 652
 653     def __init__(self, xml=None):
 654         # we need information from the gerald config.xml
 655         self.results = {}
 656
 657         if xml is not None:
 658             self.set_elements(xml)
 659
 660     def __len__(self):
 661         return len(self.results)
 662
 663     def keys(self):
 664         return self.results.keys()
 665
 666     def values(self):
 667         return self.results.values()
 668
 669     def items(self):
 670         return self.results.items()
 671
 672     def __getitem__(self, key):
 673         return self.results[key]
 674
 675     def get_elements(self):
 676         root = ElementTree.Element(ELAND.ELAND,
 677                                    {'version': unicode(ELAND.XML_VERSION)})
 678         for lane_id, lane in self.results.items():
 679             eland_lane = lane.get_elements()
 680             eland_lane.attrib[ELAND.LANE_ID] = unicode(lane_id)
 681             root.append(eland_lane)
 682         return root
 683
 684     def set_elements(self, tree):
 685         if tree.tag.lower() != ELAND.ELAND.lower():
 686             raise ValueError('Expecting %s', ELAND.ELAND)
 687         for element in list(tree):
 688             lane_id = element.attrib[ELAND.LANE_ID]
 689             lane = ElandLane(xml=element)
 690             self.results[lane_id] = lane
 691
 692 def eland(basedir, gerald=None, genome_maps=None):
 693     e = ELAND()
 694
 695     file_list = glob(os.path.join(basedir, "*_eland_result.txt"))
 696     if len(file_list) == 0:
 697         # lets handle compressed eland files too
 698         file_list = glob(os.path.join(basedir, "*_eland_result.txt.bz2"))
 699
 700     for pathname in file_list:
 701         # yes the lane_id is also being computed in ElandLane._update
 702         # I didn't want to clutter up my constructor
 703         # but I needed to persist the sample_name/lane_id for
 704         # runfolder summary_report
 705         path, name = os.path.split(pathname)
 706         split_name = name.split('_')
 707         lane_id = split_name[1]
 708
 709         if genome_maps is not None:
 710             genome_map = genome_maps[lane_id]
 711         elif gerald is not None:
 712             genome_dir = gerald.lanes[lane_id].eland_genome
 713             genome_map = build_genome_fasta_map(genome_dir)
 714         else:
 715             genome_map = {}
 716
 717         eland_result = ElandLane(pathname, genome_map)
 718         e.results[lane_id] = eland_result
 719     return e