htsworkflow/pipelines/runfolder.py

   1 """
   2 Core information needed to inspect a runfolder.
   3 """
   4 from glob import glob
   5 import logging
   6 import os
   7 import re
   8 import shutil
   9 import stat
  10 import subprocess
  11 import sys
  12 import time
  13
  14 try:
  15   from xml.etree import ElementTree
  16 except ImportError, e:
  17   from elementtree import ElementTree
  18
  19 EUROPEAN_STRPTIME = "%d-%m-%Y"
  20 EUROPEAN_DATE_RE = "([0-9]{1,2}-[0-9]{1,2}-[0-9]{4,4})"
  21 VERSION_RE = "([0-9\.]+)"
  22 USER_RE = "([a-zA-Z0-9]+)"
  23 LANES_PER_FLOWCELL = 8
  24
  25 from htsworkflow.util.alphanum import alphanum
  26 from htsworkflow.util.ethelp import indent, flatten
  27
  28 class PipelineRun(object):
  29     """
  30     Capture "interesting" information about a pipeline run
  31     """
  32     XML_VERSION = 1
  33     PIPELINE_RUN = 'PipelineRun'
  34     FLOWCELL_ID = 'FlowcellID'
  35
  36     def __init__(self, pathname=None, xml=None):
  37         if pathname is not None:
  38           self.pathname = os.path.normpath(pathname)
  39         else:
  40           self.pathname = None
  41         self._name = None
  42         self._flowcell_id = None
  43         self.image_analysis = None
  44         self.bustard = None
  45         self.gerald = None
  46
  47         if xml is not None:
  48           self.set_elements(xml)
  49
  50     def _get_flowcell_id(self):
  51         # extract flowcell ID
  52         if self._flowcell_id is None:
  53           config_dir = os.path.join(self.pathname, 'Config')
  54           flowcell_id_path = os.path.join(config_dir, 'FlowcellId.xml')
  55           if os.path.exists(flowcell_id_path):
  56             flowcell_id_tree = ElementTree.parse(flowcell_id_path)
  57             self._flowcell_id = flowcell_id_tree.findtext('Text')
  58           else:
  59             path_fields = self.pathname.split('_')
  60             if len(path_fields) > 0:
  61               # guessing last element of filename
  62               flowcell_id = path_fields[-1]
  63             else:
  64               flowcell_id = 'unknown'
  65
  66             logging.warning(
  67               "Flowcell id was not found, guessing %s" % (
  68                  flowcell_id))
  69             self._flowcell_id = flowcell_id
  70         return self._flowcell_id
  71     flowcell_id = property(_get_flowcell_id)
  72
  73     def get_elements(self):
  74         """
  75         make one master xml file from all of our sub-components.
  76         """
  77         root = ElementTree.Element(PipelineRun.PIPELINE_RUN)
  78         flowcell = ElementTree.SubElement(root, PipelineRun.FLOWCELL_ID)
  79         flowcell.text = self.flowcell_id
  80         root.append(self.image_analysis.get_elements())
  81         root.append(self.bustard.get_elements())
  82         root.append(self.gerald.get_elements())
  83         return root
  84
  85     def set_elements(self, tree):
  86         # this file gets imported by all the others,
  87         # so we need to hide the imports to avoid a cyclic imports
  88         from htsworkflow.pipelines import firecrest
  89         from htsworkflow.pipelines import ipar
  90         from htsworkflow.pipelines import bustard
  91         from htsworkflow.pipelines import gerald
  92
  93         tag = tree.tag.lower()
  94         if tag != PipelineRun.PIPELINE_RUN.lower():
  95           raise ValueError('Pipeline Run Expecting %s got %s' % (
  96               PipelineRun.PIPELINE_RUN, tag))
  97         for element in tree:
  98           tag = element.tag.lower()
  99           if tag == PipelineRun.FLOWCELL_ID.lower():
 100             self._flowcell_id = element.text
 101           #ok the xword.Xword.XWORD pattern for module.class.constant is lame
 102           # you should only have Firecrest or IPAR, never both of them.
 103           elif tag == firecrest.Firecrest.FIRECREST.lower():
 104             self.image_analysis = firecrest.Firecrest(xml=element)
 105           elif tag == ipar.IPAR.IPAR.lower():
 106             self.image_analysis = ipar.IPAR(xml=element)
 107           elif tag == bustard.Bustard.BUSTARD.lower():
 108             self.bustard = bustard.Bustard(xml=element)
 109           elif tag == gerald.Gerald.GERALD.lower():
 110             self.gerald = gerald.Gerald(xml=element)
 111           else:
 112             logging.warn('PipelineRun unrecognized tag %s' % (tag,))
 113
 114     def _get_run_name(self):
 115         """
 116         Given a run tuple, find the latest date and use that as our name
 117         """
 118         if self._name is None:
 119           tmax = max(self.image_analysis.time, self.bustard.time, self.gerald.time)
 120           timestamp = time.strftime('%Y-%m-%d', time.localtime(tmax))
 121           self._name = 'run_'+self.flowcell_id+"_"+timestamp+'.xml'
 122         return self._name
 123     name = property(_get_run_name)
 124
 125     def save(self, destdir=None):
 126         if destdir is None:
 127             destdir = ''
 128         logging.info("Saving run report "+ self.name)
 129         xml = self.get_elements()
 130         indent(xml)
 131         dest_pathname = os.path.join(destdir, self.name)
 132         ElementTree.ElementTree(xml).write(dest_pathname)
 133
 134     def load(self, filename):
 135         logging.info("Loading run report from " + filename)
 136         tree = ElementTree.parse(filename).getroot()
 137         self.set_elements(tree)
 138
 139 def load_pipeline_run_xml(pathname):
 140     """
 141     Load and instantiate a Pipeline run from a run xml file
 142
 143     :Parameters:
 144       - `pathname` : location of an run xml file
 145
 146     :Returns: initialized PipelineRun object
 147     """
 148     tree = ElementTree.parse(pathname).getroot()
 149     run = PipelineRun(xml=tree)
 150     return run
 151
 152 def get_runs(runfolder):
 153     """
 154     Search through a run folder for all the various sub component runs
 155     and then return a PipelineRun for each different combination.
 156
 157     For example if there are two different GERALD runs, this will
 158     generate two different PipelineRun objects, that differ
 159     in there gerald component.
 160     """
 161     from htsworkflow.pipelines import firecrest
 162     from htsworkflow.pipelines import ipar
 163     from htsworkflow.pipelines import bustard
 164     from htsworkflow.pipelines import gerald
 165
 166     def scan_post_image_analysis(runs, runfolder, image_analysis, pathname):
 167         logging.info("Looking for bustard directories in %s" % (pathname,))
 168         bustard_glob = os.path.join(pathname, "Bustard*")
 169         for bustard_pathname in glob(bustard_glob):
 170             logging.info("Found bustard directory %s" % (bustard_pathname,))
 171             b = bustard.bustard(bustard_pathname)
 172             gerald_glob = os.path.join(bustard_pathname, 'GERALD*')
 173             logging.info("Looking for gerald directories in %s" % (pathname,))
 174             for gerald_pathname in glob(gerald_glob):
 175                 logging.info("Found gerald directory %s" % (gerald_pathname,))
 176                 try:
 177                     g = gerald.gerald(gerald_pathname)
 178                     p = PipelineRun(runfolder)
 179                     p.image_analysis = image_analysis
 180                     p.bustard = b
 181                     p.gerald = g
 182                     runs.append(p)
 183                 except IOError, e:
 184                     logging.error("Ignoring " + str(e))
 185
 186     datadir = os.path.join(runfolder, 'Data')
 187
 188     logging.info('Searching for runs in ' + datadir)
 189     runs = []
 190     # scan for firecrest directories
 191     for firecrest_pathname in glob(os.path.join(datadir,"*Firecrest*")):
 192         logging.info('Found firecrest in ' + datadir)
 193         image_analysis = firecrest.firecrest(firecrest_pathname)
 194         if image_analysis is None:
 195             logging.warn(
 196                 "%s is an empty or invalid firecrest directory" % (firecrest_pathname,)
 197             )
 198         else:
 199             scan_post_image_analysis(
 200                 runs, runfolder, image_analysis, firecrest_pathname
 201             )
 202     # scan for IPAR directories
 203     for ipar_pathname in glob(os.path.join(datadir,"IPAR_*")):
 204         logging.info('Found ipar directories in ' + datadir)
 205         image_analysis = ipar.ipar(ipar_pathname)
 206         if image_analysis is None:
 207             logging.warn(
 208                 "%s is an empty or invalid IPAR directory" %(ipar_pathname,)
 209             )
 210         else:
 211             scan_post_image_analysis(
 212                 runs, runfolder, image_analysis, ipar_pathname
 213             )
 214
 215     return runs
 216
 217 def get_specific_run(gerald_dir):
 218     """
 219     Given a gerald directory, construct a PipelineRun out of its parents
 220
 221     Basically this allows specifying a particular run instead of the previous
 222     get_runs which scans a runfolder for various combinations of
 223     firecrest/ipar/bustard/gerald runs.
 224     """
 225     from htsworkflow.pipelines import firecrest
 226     from htsworkflow.pipelines import ipar
 227     from htsworkflow.pipelines import bustard
 228     from htsworkflow.pipelines import gerald
 229
 230     bustard_dir = os.path.abspath(os.path.join(gerald_dir, '..'))
 231     image_dir = os.path.abspath(os.path.join(gerald_dir, '..', '..'))
 232
 233     runfolder_dir = os.path.abspath(os.path.join(image_dir, '..','..'))
 234
 235     logging.debug('--- use-run detected options ---')
 236     logging.debug('runfolder: %s' % (runfolder_dir,))
 237     logging.debug('image_dir: %s' % (image_dir,))
 238     logging.debug('bustard_dir: %s' % (bustard_dir,))
 239     logging.debug('gerald_dir: %s' % (gerald_dir,))
 240
 241     # find our processed image dir
 242     image_run = ipar.ipar(image_dir)
 243     if image_run is None:
 244         image_run = firecrest.firecrest(image_dir)
 245     if image_run is None:
 246         msg = '%s does not contain an image processing step' % (image_dir,)
 247         logging.error(msg)
 248         return None
 249
 250     # find our base calling
 251     base_calling_run = bustard.bustard(bustard_dir)
 252     if base_calling_run is None:
 253         logging.error('%s does not contain a bustard run' % (bustard_dir,))
 254         return None
 255
 256     # find alignments
 257     gerald_run = gerald.gerald(gerald_dir)
 258     if gerald_run is None:
 259         logging.error('%s does not contain a gerald run' % (gerald_dir,))
 260         return None
 261
 262     p = PipelineRun(runfolder_dir)
 263     p.image_analysis = image_run
 264     p.bustard = base_calling_run
 265     p.gerald = gerald_run
 266
 267     logging.info('Constructed PipelineRun from %s' % (gerald_dir,))
 268     return p
 269
 270 def extract_run_parameters(runs):
 271     """
 272     Search through runfolder_path for various runs and grab their parameters
 273     """
 274     for run in runs:
 275       run.save()
 276
 277 def summarize_mapped_reads(genome_map, mapped_reads):
 278     """
 279     Summarize per chromosome reads into a genome count
 280     But handle spike-in/contamination symlinks seperately.
 281     """
 282     summarized_reads = {}
 283     genome_reads = 0
 284     genome = 'unknown'
 285     for k, v in mapped_reads.items():
 286         path, k = os.path.split(k)
 287         if len(path) > 0 and not genome_map.has_key(path):
 288             genome = path
 289             genome_reads += v
 290         else:
 291             summarized_reads[k] = summarized_reads.setdefault(k, 0) + v
 292     summarized_reads[genome] = genome_reads
 293     return summarized_reads
 294
 295 def summarize_lane(gerald, lane_id):
 296     report = []
 297     summary_results = gerald.summary.lane_results
 298     for end in range(len(summary_results)):
 299       eland_result = gerald.eland_results.results[end][lane_id]
 300       report.append("Sample name %s" % (eland_result.sample_name))
 301       report.append("Lane id %s end %s" % (eland_result.lane_id, end))
 302       cluster = summary_results[end][eland_result.lane_id].cluster
 303       report.append("Clusters %d +/- %d" % (cluster[0], cluster[1]))
 304       report.append("Total Reads: %d" % (eland_result.reads))
 305       mc = eland_result._match_codes
 306       nm = mc['NM']
 307       nm_percent = float(nm)/eland_result.reads  * 100
 308       qc = mc['QC']
 309       qc_percent = float(qc)/eland_result.reads * 100
 310
 311       report.append("No Match: %d (%2.2g %%)" % (nm, nm_percent))
 312       report.append("QC Failed: %d (%2.2g %%)" % (qc, qc_percent))
 313       report.append('Unique (0,1,2 mismatches) %d %d %d' % \
 314                     (mc['U0'], mc['U1'], mc['U2']))
 315       report.append('Repeat (0,1,2 mismatches) %d %d %d' % \
 316                     (mc['R0'], mc['R1'], mc['R2']))
 317       report.append("Mapped Reads")
 318       mapped_reads = summarize_mapped_reads(eland_result.genome_map, eland_result.mapped_reads)
 319       for name, counts in mapped_reads.items():
 320         report.append("  %s: %d" % (name, counts))
 321       report.append('')
 322     return report
 323
 324 def summary_report(runs):
 325     """
 326     Summarize cluster numbers and mapped read counts for a runfolder
 327     """
 328     report = []
 329     for run in runs:
 330         # print a run name?
 331         report.append('Summary for %s' % (run.name,))
 332         # sort the report
 333         eland_keys = run.gerald.eland_results.results[0].keys()
 334         eland_keys.sort(alphanum)
 335
 336         for lane_id in eland_keys:
 337             report.extend(summarize_lane(run.gerald, lane_id))
 338             report.append('---')
 339             report.append('')
 340         return os.linesep.join(report)
 341
 342 def is_compressed(filename):
 343     if os.path.splitext(filename)[1] == ".gz":
 344         return True
 345     elif os.path.splitext(filename)[1] == '.bz2':
 346         return True
 347     else:
 348         return False
 349
 350 def extract_results(runs, output_base_dir=None):
 351     if output_base_dir is None:
 352         output_base_dir = os.getcwd()
 353
 354     for r in runs:
 355       result_dir = os.path.join(output_base_dir, r.flowcell_id)
 356       logging.info("Using %s as result directory" % (result_dir,))
 357       if not os.path.exists(result_dir):
 358         os.mkdir(result_dir)
 359
 360       # create cycle_dir
 361       cycle = "C%d-%d" % (r.image_analysis.start, r.image_analysis.stop)
 362       logging.info("Filling in %s" % (cycle,))
 363       cycle_dir = os.path.join(result_dir, cycle)
 364       if os.path.exists(cycle_dir):
 365         logging.error("%s already exists, not overwriting" % (cycle_dir,))
 366         continue
 367       else:
 368         os.mkdir(cycle_dir)
 369
 370       # copy stuff out of the main run
 371       g = r.gerald
 372
 373       # save run file
 374       r.save(cycle_dir)
 375
 376       return
 377
 378       # Copy Summary.htm
 379       summary_path = os.path.join(r.gerald.pathname, 'Summary.htm')
 380       if os.path.exists(summary_path):
 381           logging.info('Copying %s to %s' % (summary_path, cycle_dir))
 382           shutil.copy(summary_path, cycle_dir)
 383       else:
 384           logging.info('Summary file %s was not found' % (summary_path,))
 385
 386       # tar score files
 387       score_files = []
 388
 389       # check for g.pathname/Temp a new feature of 1.1rc1
 390       scores_path = g.pathname
 391       scores_path_temp = os.path.join(scores_path, 'Temp')
 392       if os.path.isdir(scores_path_temp):
 393           scores_path = scores_path_temp
 394
 395       # hopefully we have a directory that contains s_*_score files
 396       for f in os.listdir(scores_path):
 397           if re.match('.*_score.txt', f):
 398               score_files.append(f)
 399
 400       tar_cmd = ['/bin/tar', 'c'] + score_files
 401       bzip_cmd = [ 'bzip2', '-9', '-c' ]
 402       tar_dest_name =os.path.join(cycle_dir, 'scores.tar.bz2')
 403       tar_dest = open(tar_dest_name, 'w')
 404       logging.info("Compressing score files from %s" % (scores_path,))
 405       logging.info("Running tar: " + " ".join(tar_cmd[:10]))
 406       logging.info("Running bzip2: " + " ".join(bzip_cmd))
 407       logging.info("Writing to %s" %(tar_dest_name))
 408
 409       tar = subprocess.Popen(tar_cmd, stdout=subprocess.PIPE, shell=False,
 410                              cwd=scores_path)
 411       bzip = subprocess.Popen(bzip_cmd, stdin=tar.stdout, stdout=tar_dest)
 412       tar.wait()
 413
 414       # copy & bzip eland files
 415       for lanes_dictionary in g.eland_results.results:
 416           for eland_lane in lanes_dictionary.values():
 417               source_name = eland_lane.pathname
 418               path, name = os.path.split(eland_lane.pathname)
 419               dest_name = os.path.join(cycle_dir, name)
 420               logging.info("Saving eland file %s to %s" % \
 421                            (source_name, dest_name))
 422
 423               if is_compressed(name):
 424                 logging.info('Already compressed, Saving to %s' % (dest_name, ))
 425                 shutil.copy(source_name, dest_name)
 426               else:
 427                 # not compressed
 428                 dest_name += '.bz2'
 429                 args = ['bzip2', '-9', '-c', source_name]
 430                 logging.info('Running: %s' % ( " ".join(args) ))
 431                 bzip_dest = open(dest_name, 'w')
 432                 bzip = subprocess.Popen(args, stdout=bzip_dest)
 433                 logging.info('Saving to %s' % (dest_name, ))
 434                 bzip.wait()
 435
 436 def clean_runs(runs):
 437     """
 438     Clean up run folders to optimize for compression.
 439     """
 440     # TODO: implement this.
 441     # rm RunLog*.xml
 442     # rm pipeline_*.txt
 443     # rm gclog.txt
 444     # rm NetCopy.log
 445     # rm nfn.log
 446     # rm Images/L*
 447     # cd Data/C1-*_Firecrest*
 448     # make clean_intermediate
 449
 450     pass