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 get_runs(runfolder):
 140     """
 141     Search through a run folder for all the various sub component runs
 142     and then return a PipelineRun for each different combination.
 143
 144     For example if there are two different GERALD runs, this will
 145     generate two different PipelineRun objects, that differ
 146     in there gerald component.
 147     """
 148     from htsworkflow.pipelines import firecrest
 149     from htsworkflow.pipelines import ipar
 150     from htsworkflow.pipelines import bustard
 151     from htsworkflow.pipelines import gerald
 152
 153     def scan_post_image_analysis(runs, runfolder, image_analysis, pathname):
 154         logging.info("Looking for bustard directories in %s" % (pathname,))
 155         bustard_glob = os.path.join(pathname, "Bustard*")
 156         for bustard_pathname in glob(bustard_glob):
 157             logging.info("Found bustard directory %s" % (bustard_pathname,))
 158             b = bustard.bustard(bustard_pathname)
 159             gerald_glob = os.path.join(bustard_pathname, 'GERALD*')
 160             logging.info("Looking for gerald directories in %s" % (pathname,))
 161             for gerald_pathname in glob(gerald_glob):
 162                 logging.info("Found gerald directory %s" % (gerald_pathname,))
 163                 try:
 164                     g = gerald.gerald(gerald_pathname)
 165                     p = PipelineRun(runfolder)
 166                     p.image_analysis = image_analysis
 167                     p.bustard = b
 168                     p.gerald = g
 169                     runs.append(p)
 170                 except IOError, e:
 171                     print "Ignoring", str(e)
 172
 173     datadir = os.path.join(runfolder, 'Data')
 174
 175     logging.info('Searching for runs in ' + datadir)
 176     runs = []
 177     # scan for firecrest directories
 178     for firecrest_pathname in glob(os.path.join(datadir,"*Firecrest*")):
 179         logging.info('Found firecrest in ' + datadir)
 180         image_analysis = firecrest.firecrest(firecrest_pathname)
 181         scan_post_image_analysis(runs, runfolder, image_analysis, firecrest_pathname)
 182     # scan for IPAR directories
 183     for ipar_pathname in glob(os.path.join(datadir,"IPAR_*")):
 184         logging.info('Found ipar directories in ' + datadir)
 185         image_analysis = ipar.ipar(ipar_pathname)
 186         scan_post_image_analysis(runs, runfolder, image_analysis, ipar_pathname)
 187
 188     return runs
 189
 190
 191 def extract_run_parameters(runs):
 192     """
 193     Search through runfolder_path for various runs and grab their parameters
 194     """
 195     for run in runs:
 196       run.save()
 197
 198 def summarize_mapped_reads(mapped_reads):
 199     """
 200     Summarize per chromosome reads into a genome count
 201     But handle spike-in/contamination symlinks seperately.
 202     """
 203     summarized_reads = {}
 204     genome_reads = 0
 205     genome = 'unknown'
 206     for k, v in mapped_reads.items():
 207         path, k = os.path.split(k)
 208         if len(path) > 0:
 209             genome = path
 210             genome_reads += v
 211         else:
 212             summarized_reads[k] = summarized_reads.setdefault(k, 0) + v
 213     summarized_reads[genome] = genome_reads
 214     return summarized_reads
 215
 216 def summarize_lane(gerald, lane_id):
 217     report = []
 218     summary_results = gerald.summary.lane_results
 219     for end in range(len(summary_results)):
 220       eland_result = gerald.eland_results.results[end][lane_id]
 221       report.append("Sample name %s" % (eland_result.sample_name))
 222       report.append("Lane id %s end %s" % (eland_result.lane_id, end))
 223       cluster = summary_results[end][eland_result.lane_id].cluster
 224       report.append("Clusters %d +/- %d" % (cluster[0], cluster[1]))
 225       report.append("Total Reads: %d" % (eland_result.reads))
 226       mc = eland_result._match_codes
 227       nm = mc['NM']
 228       nm_percent = float(nm)/eland_result.reads  * 100
 229       qc = mc['QC']
 230       qc_percent = float(qc)/eland_result.reads * 100
 231
 232       report.append("No Match: %d (%2.2g %%)" % (nm, nm_percent))
 233       report.append("QC Failed: %d (%2.2g %%)" % (qc, qc_percent))
 234       report.append('Unique (0,1,2 mismatches) %d %d %d' % \
 235                     (mc['U0'], mc['U1'], mc['U2']))
 236       report.append('Repeat (0,1,2 mismatches) %d %d %d' % \
 237                     (mc['R0'], mc['R1'], mc['R2']))
 238       report.append("Mapped Reads")
 239       mapped_reads = summarize_mapped_reads(eland_result.mapped_reads)
 240       for name, counts in mapped_reads.items():
 241         report.append("  %s: %d" % (name, counts))
 242       report.append('')
 243     return report
 244
 245 def summary_report(runs):
 246     """
 247     Summarize cluster numbers and mapped read counts for a runfolder
 248     """
 249     report = []
 250     for run in runs:
 251         # print a run name?
 252         report.append('Summary for %s' % (run.name,))
 253         # sort the report
 254         eland_keys = run.gerald.eland_results.results[0].keys()
 255         eland_keys.sort(alphanum)
 256
 257         for lane_id in eland_keys:
 258             report.extend(summarize_lane(run.gerald, lane_id))
 259             report.append('---')
 260             report.append('')
 261         return os.linesep.join(report)
 262
 263 def is_compressed(filename):
 264     if os.path.splitext(filename)[1] == ".gz":
 265         return True
 266     elif os.path.splitext(filename)[1] == '.bz2':
 267         return True
 268     else:
 269         return False
 270
 271 def extract_results(runs, output_base_dir=None):
 272     if output_base_dir is None:
 273         output_base_dir = os.getcwd()
 274
 275     for r in runs:
 276       result_dir = os.path.join(output_base_dir, r.flowcell_id)
 277       logging.info("Using %s as result directory" % (result_dir,))
 278       if not os.path.exists(result_dir):
 279         os.mkdir(result_dir)
 280
 281       # create cycle_dir
 282       cycle = "C%d-%d" % (r.image_analysis.start, r.image_analysis.stop)
 283       logging.info("Filling in %s" % (cycle,))
 284       cycle_dir = os.path.join(result_dir, cycle)
 285       if os.path.exists(cycle_dir):
 286         logging.error("%s already exists, not overwriting" % (cycle_dir,))
 287         continue
 288       else:
 289         os.mkdir(cycle_dir)
 290
 291       # copy stuff out of the main run
 292       g = r.gerald
 293
 294       # save run file
 295       r.save(cycle_dir)
 296
 297       # Copy Summary.htm
 298       summary_path = os.path.join(r.gerald.pathname, 'Summary.htm')
 299       if os.path.exists(summary_path):
 300           logging.info('Copying %s to %s' % (summary_path, cycle_dir))
 301           shutil.copy(summary_path, cycle_dir)
 302       else:
 303           logging.info('Summary file %s was not found' % (summary_path,))
 304
 305       # tar score files
 306       score_files = []
 307       for f in os.listdir(g.pathname):
 308           if re.match('.*_score.txt', f):
 309               score_files.append(f)
 310
 311       tar_cmd = ['/bin/tar', 'c'] + score_files
 312       bzip_cmd = [ 'bzip2', '-9', '-c' ]
 313       tar_dest_name =os.path.join(cycle_dir, 'scores.tar.bz2')
 314       tar_dest = open(tar_dest_name, 'w')
 315       logging.info("Compressing score files in %s" % (g.pathname,))
 316       logging.info("Running tar: " + " ".join(tar_cmd[:10]))
 317       logging.info("Running bzip2: " + " ".join(bzip_cmd))
 318       logging.info("Writing to %s" %(tar_dest_name))
 319
 320       tar = subprocess.Popen(tar_cmd, stdout=subprocess.PIPE, shell=False, cwd=g.pathname)
 321       bzip = subprocess.Popen(bzip_cmd, stdin=tar.stdout, stdout=tar_dest)
 322       tar.wait()
 323
 324       # copy & bzip eland files
 325       for lanes_dictionary in g.eland_results.results:
 326           for eland_lane in lanes_dictionary.values():
 327               source_name = eland_lane.pathname
 328               path, name = os.path.split(eland_lane.pathname)
 329               dest_name = os.path.join(cycle_dir, name)
 330               if is_compressed(name):
 331                 logging.info('Already compressed, Saving to %s' % (dest_name, ))
 332                 shutil.copy(source_name, dest_name)
 333               else:
 334                 # not compressed
 335                 dest_name += '.bz2'
 336                 args = ['bzip2', '-9', '-c', source_name]
 337                 logging.info('Running: %s' % ( " ".join(args) ))
 338                 bzip_dest = open(dest_name, 'w')
 339                 bzip = subprocess.Popen(args, stdout=bzip_dest)
 340                 logging.info('Saving to %s' % (dest_name, ))
 341                 bzip.wait()
 342
 343 def clean_runs(runs):
 344     """
 345     Clean up run folders to optimize for compression.
 346     """
 347     # TODO: implement this.
 348     # rm RunLog*.xml
 349     # rm pipeline_*.txt
 350     # rm gclog.txt
 351     # rm NetCopy.log
 352     # rm nfn.log
 353     # rm Images/L*
 354     # cd Data/C1-*_Firecrest*
 355     # make clean_intermediate
 356
 357     pass