htsworkflow/pipelines/sequences.py

   1 """
   2 Utilities to work with the various eras of sequence archive files
   3 """
   4 import collections
   5 import logging
   6 import os
   7 import types
   8 import re
   9 import sys
  10 from urlparse import urljoin, urlparse
  11
  12 import RDF
  13 from htsworkflow.util.rdfhelp import libraryOntology as libNS
  14 from htsworkflow.util.rdfhelp import toTypedNode, fromTypedNode, rdfNS, \
  15      strip_namespace, dump_model, simplify_uri
  16
  17 LOGGER = logging.getLogger(__name__)
  18
  19 eland_re = re.compile('s_(?P<lane>\d)(_(?P<read>\d))?_eland_')
  20 raw_seq_re = re.compile('woldlab_[0-9]{6}_[^_]+_[\d]+_[\dA-Za-z]+')
  21 qseq_re = re.compile('woldlab_[0-9]{6}_[^_]+_[\d]+_[\dA-Za-z]+_l[\d]_r[\d].tar.bz2')
  22
  23 SEQUENCE_TABLE_NAME = "sequences"
  24 def create_sequence_table(cursor):
  25     """
  26     Create a SQL table to hold  SequenceFile entries
  27     """
  28     sql = """
  29 CREATE TABLE %(table)s (
  30   filetype   CHAR(8),
  31   path       TEXT,
  32   flowcell   CHAR(8),
  33   lane       INTEGER,
  34   read       INTEGER,
  35   pf         BOOLEAN,
  36   cycle      CHAR(8)
  37 );
  38 """ %( {'table': SEQUENCE_TABLE_NAME} )
  39     return cursor.execute(sql)
  40
  41 FlowcellPath = collections.namedtuple('FlowcellPath',
  42                                       'flowcell start stop project')
  43
  44 class SequenceFile(object):
  45     """
  46     Simple container class that holds the path to a sequence archive
  47     and basic descriptive information.
  48     """
  49     def __init__(self, filetype, path, flowcell, lane,
  50                  read=None,
  51                  pf=None,
  52                  cycle=None,
  53                  project=None,
  54                  index=None,
  55                  split=None):
  56         """Store various fields used in our sequence files
  57
  58         filetype is one of 'qseq', 'srf', 'fastq'
  59         path = location of file
  60         flowcell = files flowcell id
  61         lane = which lane
  62         read = which sequencer read, usually 1 or 2
  63         pf = did it pass filter
  64         cycle = cycle dir name e.g. C1-202
  65         project = projed name from HiSeq, probably library ID
  66         index = HiSeq barcode index sequence
  67         split = file fragment from HiSeq (Since one file is split into many)
  68         """
  69         self.filetype = filetype
  70         self.path = path
  71         self.flowcell = flowcell
  72         self.lane = lane
  73         self.read = read
  74         self.pf = pf
  75         self.cycle = cycle
  76         self.project = project
  77         self.index = index
  78         self.split = split
  79
  80     def __hash__(self):
  81         return hash(self.key())
  82
  83     def key(self):
  84         return (self.flowcell, self.lane, self.read, self.project, self.split)
  85
  86     def __unicode__(self):
  87         return unicode(self.path)
  88
  89     def __eq__(self, other):
  90         """
  91         Equality is defined if everything but the path matches
  92         """
  93         attributes = ['filetype',
  94                       'flowcell',
  95                       'lane',
  96                       'read',
  97                       'pf',
  98                       'cycle',
  99                       'project',
 100                       'index',
 101                       'split']
 102         for a in attributes:
 103             if getattr(self, a) != getattr(other, a):
 104                 return False
 105
 106         return True
 107
 108     def __ne__(self, other):
 109         return not self == other
 110
 111     def __repr__(self):
 112         return u"<%s %s %s %s>" % (self.filetype, self.flowcell, self.lane, self.path)
 113
 114     def make_target_name(self, root):
 115         """
 116         Create target name for where we need to link this sequence too
 117         """
 118         path, basename = os.path.split(self.path)
 119         # Because the names aren't unque we include the flowcel name
 120         # because there were different eland files for different length
 121         # analyses, we include the cycle length in the name.
 122         if self.filetype == 'eland':
 123             template = "%(flowcell)s_%(cycle)s_%(eland)s"
 124             basename = template % { 'flowcell': self.flowcell,
 125                                     'cycle': self.cycle,
 126                                     'eland': basename }
 127         # else:
 128         # all the other file types have names that include flowcell/lane
 129         # information and thus are unique so we don't have to do anything
 130         return os.path.join(root, basename)
 131
 132     def save_to_sql(self, cursor):
 133         """
 134         Add this entry to a DB2.0 database.
 135         """
 136         #FIXME: NEEDS SQL ESCAPING
 137         header_macro = {'table': SEQUENCE_TABLE_NAME }
 138         sql_header = "insert into %(table)s (" % header_macro
 139         sql_columns = ['filetype','path','flowcell','lane']
 140         sql_middle = ") values ("
 141         sql_values = [self.filetype, self.path, self.flowcell, self.lane]
 142         sql_footer = ");"
 143         for name in ['read', 'pf', 'cycle']:
 144             value = getattr(self, name)
 145             if value is not None:
 146                 sql_columns.append(name)
 147                 sql_values.append(value)
 148
 149         sql = " ".join([sql_header,
 150                         ", ".join(sql_columns),
 151                         sql_middle,
 152                         # note the following makes a string like ?,?,?
 153                         ",".join(["?"] * len(sql_values)),
 154                         sql_footer])
 155
 156         return cursor.execute(sql, sql_values)
 157
 158     def save_to_model(self, model, base_url=None):
 159         def add_lit(model, s, p, o):
 160             if o is not None:
 161                 model.add_statement(RDF.Statement(s, p, toTypedNode(o)))
 162         def add(model, s, p, o):
 163             model.add_statement(RDF.Statement(s,p,o))
 164         # a bit unreliable... assumes filesystem is encoded in utf-8
 165         path = os.path.abspath(self.path.encode('utf-8'))
 166         fileNode = RDF.Node(RDF.Uri('file://' + path))
 167         add(model, fileNode, rdfNS['type'], libNS['IlluminaResult'])
 168         add_lit(model, fileNode, libNS['flowcell_id'], self.flowcell)
 169         add_lit(model, fileNode, libNS['lane_number'], self.lane)
 170         if self.read is not None:
 171             add_lit(model, fileNode, libNS['read'], self.read)
 172         else:
 173             add_lit(model, fileNode, libNS['read'], '')
 174
 175         add_lit(model, fileNode, libNS['library_id'], self.project)
 176         add_lit(model, fileNode, libNS['multiplex_index'], self.index)
 177         add_lit(model, fileNode, libNS['split_id'], self.split)
 178         add_lit(model, fileNode, libNS['cycle'], self.cycle)
 179         add_lit(model, fileNode, libNS['passed_filter'], self.pf)
 180         add(model, fileNode, libNS['file_type'], libNS[self.filetype])
 181
 182         if base_url is not None:
 183             flowcell = RDF.Node(RDF.Uri("{base}/flowcell/{flowcell}/".format(
 184                 base=base_url,
 185                 flowcell=self.flowcell)))
 186             add(model, fileNode, libNS['flowcell'], flowcell)
 187             if self.project is not None:
 188                 library = RDF.Node(RDF.Uri("{base}/library/{library}".format(
 189                     base=base_url,
 190                     library=self.project)))
 191                 add(model, fileNode, libNS['library'], library)
 192
 193
 194     @classmethod
 195     def load_from_model(cls, model, seq_id):
 196         def get(s, p):
 197             values = []
 198             stmts = model.find_statements(RDF.Statement(s, p, None))
 199             for s in stmts:
 200                 obj = s.object
 201                 if not obj.is_resource():
 202                     values.append(fromTypedNode(obj))
 203                 else:
 204                     values.append(obj)
 205             return values
 206         def get_one(s, p):
 207             values = get(s, p)
 208             if len(values) > 1:
 209                 errmsg = u"To many values for %s %s"
 210                 raise ValueError(errmsg % (unicode(s), unicode(p)))
 211             elif len(values) == 1:
 212                 return values[0]
 213             else:
 214                 return None
 215
 216         if not isinstance(seq_id, RDF.Node):
 217             seq_id = RDF.Node(RDF.Uri(seq_id))
 218         result_statement = RDF.Statement(seq_id,
 219                                          rdfNS['type'],
 220                                          libNS['IlluminaResult'])
 221         if not model.contains_statement(result_statement):
 222             raise KeyError(u"%s not found" % (unicode(seq_id),))
 223
 224         seq_type_node = model.get_target(seq_id, libNS['file_type'])
 225         seq_type = strip_namespace(libNS, seq_type_node)
 226
 227         path = urlparse(str(seq_id.uri)).path
 228         flowcellNode = get_one(seq_id, libNS['flowcell'])
 229         flowcell = get_one(seq_id, libNS['flowcell_id'])
 230         lane = get_one(seq_id, libNS['lane_number'])
 231         read = get_one(seq_id, libNS['read'])
 232
 233         obj = cls(seq_type, path, flowcell, lane)
 234         obj.read = read if read != '' else None
 235         obj.project = get_one(seq_id, libNS['library_id'])
 236         obj.index = get_one(seq_id, libNS['multiplex_index'])
 237         obj.split = get_one(seq_id, libNS['split_id'])
 238         obj.cycle = get_one(seq_id, libNS['cycle'] )
 239         obj.pf = get_one(seq_id, libNS['passed_filter'])
 240         obj.libraryNode = get_one(seq_id, libNS['library'])
 241         return obj
 242
 243
 244 def get_flowcell_cycle(path):
 245     """
 246     Extract flowcell, cycle from pathname
 247     """
 248     path = os.path.normpath(path)
 249     project = None
 250     rest, tail = os.path.split(path)
 251     if tail.startswith('Project_'):
 252         # we're in a multiplexed sample
 253         project = tail
 254         rest, cycle = os.path.split(rest)
 255     else:
 256         cycle = tail
 257
 258     rest, flowcell = os.path.split(rest)
 259     cycle_match = re.match("C(?P<start>[0-9]+)-(?P<stop>[0-9]+)", cycle)
 260     if cycle_match is None:
 261         raise ValueError(
 262             "Expected .../flowcell/cycle/ directory structure in %s" % \
 263             (path,))
 264     start = cycle_match.group('start')
 265     if start is not None:
 266         start = int(start)
 267     stop = cycle_match.group('stop')
 268     if stop is not None:
 269         stop = int(stop)
 270
 271     return FlowcellPath(flowcell, start, stop, project)
 272
 273 def parse_srf(path, filename):
 274     flowcell_dir, start, stop, project = get_flowcell_cycle(path)
 275     basename, ext = os.path.splitext(filename)
 276     records = basename.split('_')
 277     flowcell = records[4]
 278     lane = records[5][0]
 279     fullpath = os.path.join(path, filename)
 280
 281     if flowcell_dir != flowcell:
 282         LOGGER.warn("flowcell %s found in wrong directory %s" % \
 283                          (flowcell, path))
 284
 285     return SequenceFile('srf', fullpath, flowcell, lane, cycle=stop)
 286
 287 def parse_qseq(path, filename):
 288     flowcell_dir, start, stop, project = get_flowcell_cycle(path)
 289     basename, ext = os.path.splitext(filename)
 290     records = basename.split('_')
 291     fullpath = os.path.join(path, filename)
 292     flowcell = records[4]
 293     lane = records[5][1]
 294     read = int(records[6][1])
 295
 296     if flowcell_dir != flowcell:
 297         LOGGER.warn("flowcell %s found in wrong directory %s" % \
 298                          (flowcell, path))
 299
 300     return SequenceFile('qseq', fullpath, flowcell, lane, read, cycle=stop)
 301
 302 def parse_fastq(path, filename):
 303     """Parse fastq names
 304     """
 305     flowcell_dir, start, stop, project = get_flowcell_cycle(path)
 306     basename = re.sub('\.fastq(\.gz|\.bz2)?$', '', filename)
 307     records = basename.split('_')
 308     fullpath = os.path.join(path, filename)
 309     if project is not None:
 310         # demultiplexed sample!
 311         flowcell = flowcell_dir
 312         lane = records[2][-1]
 313         read = int(records[3][-1])
 314         pf = True # as I understand it hiseq runs toss the ones that fail filter
 315         index = records[1]
 316         project_id = records[0]
 317         split = records[4]
 318         sequence_type = 'split_fastq'
 319     else:
 320         flowcell = records[4]
 321         lane = records[5][1]
 322         read = int(records[6][1])
 323         pf = parse_fastq_pf_flag(records)
 324         index = None
 325         project_id = None
 326         split = None
 327         sequence_type = 'fastq'
 328
 329     if flowcell_dir != flowcell:
 330         LOGGER.warn("flowcell %s found in wrong directory %s" % \
 331                          (flowcell, path))
 332
 333     return SequenceFile(sequence_type, fullpath, flowcell, lane, read,
 334                         pf=pf,
 335                         cycle=stop,
 336                         project=project_id,
 337                         index=index,
 338                         split=split)
 339
 340 def parse_fastq_pf_flag(records):
 341     """Take a fastq filename split on _ and look for the pass-filter flag
 342     """
 343     if len(records) < 8:
 344         pf = None
 345     else:
 346         fastq_type = records[-1].lower()
 347         if fastq_type.startswith('pass'):
 348             pf = True
 349         elif fastq_type.startswith('nopass'):
 350             pf = False
 351         elif fastq_type.startswith('all'):
 352             pf = None
 353         else:
 354             raise ValueError("Unrecognized fastq name: %s" % (
 355                 "_".join(records),))
 356
 357     return pf
 358
 359 def parse_eland(path, filename, eland_match=None):
 360     if eland_match is None:
 361         eland_match = eland_re.match(filename)
 362     fullpath = os.path.join(path, filename)
 363     flowcell, start, stop, project = get_flowcell_cycle(path)
 364     if eland_match.group('lane'):
 365         lane = eland_match.group('lane')
 366     else:
 367         lane = None
 368     if eland_match.group('read'):
 369         read = int(eland_match.group('read'))
 370     else:
 371         read = None
 372     return SequenceFile('eland', fullpath, flowcell, lane, read, cycle=stop)
 373
 374 def scan_for_sequences(dirs):
 375     """
 376     Scan through a list of directories for sequence like files
 377     """
 378     sequences = []
 379     if type(dirs) in types.StringTypes:
 380         raise ValueError("You probably want a list or set, not a string")
 381
 382     for d in dirs:
 383         LOGGER.info("Scanning %s for sequences" % (d,))
 384         if not os.path.exists(d):
 385             LOGGER.warn("Flowcell directory %s does not exist" % (d,))
 386             continue
 387
 388         for path, dirname, filenames in os.walk(d):
 389             for f in filenames:
 390                 seq = None
 391                 # find sequence files
 392                 if f.endswith('.md5'):
 393                     continue
 394                 elif f.endswith('.srf') or f.endswith('.srf.bz2'):
 395                     seq = parse_srf(path, f)
 396                 elif qseq_re.match(f):
 397                     seq = parse_qseq(path, f)
 398                 elif f.endswith('.fastq') or \
 399                      f.endswith('.fastq.bz2') or \
 400                      f.endswith('.fastq.gz'):
 401                     seq = parse_fastq(path, f)
 402                 eland_match = eland_re.match(f)
 403                 if eland_match:
 404                     if f.endswith('.md5'):
 405                         continue
 406                     seq = parse_eland(path, f, eland_match)
 407                 if seq:
 408                     sequences.append(seq)
 409                     LOGGER.debug("Found sequence at %s" % (f,))
 410
 411     return sequences
 412
 413
 414 def update_model_sequence_library(model, base_url):
 415     """Find sequence objects and add library information if its missing
 416     """
 417     file_body = """
 418     prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 419     select ?filenode ?flowcell_id ?lane_id ?library_id ?flowcell ?library
 420     where {
 421        ?filenode a libns:IlluminaResult ;
 422                  libns:flowcell_id ?flowcell_id ;
 423                  libns:lane_number ?lane_id .
 424        OPTIONAL { ?filenode libns:flowcell ?flowcell . }
 425        OPTIONAL { ?filenode libns:library ?library .}
 426        OPTIONAL { ?filenode libns:library_id ?library_id .}
 427     }
 428     """
 429     LOGGER.debug("update_model_sequence_library query %s", file_body)
 430     file_query = RDF.SPARQLQuery(file_body)
 431     files = file_query.execute(model)
 432
 433     libraryNS = RDF.NS(urljoin(base_url, 'library/'))
 434     flowcellNS = RDF.NS(urljoin(base_url, 'flowcell/'))
 435     for f in files:
 436         filenode = f['filenode']
 437         LOGGER.debug("Updating file node %s", str(filenode))
 438         lane_id = fromTypedNode(f['lane_id'])
 439         if f['flowcell'] is None:
 440             flowcell = flowcellNS[str(f['flowcell_id'])+'/']
 441             LOGGER.debug("Adding file (%s) to flowcell (%s) link",
 442                          str(filenode),
 443                          str(flowcell))
 444             model.add_statement(
 445                 RDF.Statement(filenode, libNS['flowcell'], flowcell))
 446         else:
 447             flowcell = f['flowcell']
 448
 449         if f['library'] is None:
 450             if f['library_id'] is not None:
 451                 library = libraryNS[str(f['library_id']) + '/']
 452             else:
 453                 library = guess_library_from_model(model, base_url,
 454                                                    flowcell,
 455                                                    lane_id)
 456                 if library is None:
 457                     LOGGER.error("Unable to decypher: %s %s",
 458                                  str(flowcell), str(lane_id))
 459                     continue
 460                 library_id = toTypedNode(simplify_uri(library))
 461                 LOGGER.debug("Adding file (%s) to library (%s) link",
 462                              str(filenode),
 463                              str(library))
 464                 model.add_statement(
 465                     RDF.Statement(filenode, libNS['library_id'], library_id))
 466             if library is not None:
 467                 model.add_statement(
 468                     RDF.Statement(filenode, libNS['library'], library))
 469
 470
 471 def guess_library_from_model(model, base_url, flowcell, lane_id):
 472     """Attempt to find library URI
 473     """
 474     flowcellNode = RDF.Node(flowcell)
 475     flowcell = str(flowcell.uri)
 476     lane_body = """
 477     prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 478     prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 479     prefix xsd: <http://www.w3.org/2001/XMLSchema#>
 480
 481     select ?library ?lane
 482     where {{
 483       <{flowcell}> libns:has_lane ?lane ;
 484                    a libns:IlluminaFlowcell .
 485       ?lane libns:lane_number ?lane_id ;
 486             libns:library ?library .
 487       FILTER(str(?lane_id) = "{lane_id}")
 488     }}
 489     """
 490     lane_body = lane_body.format(flowcell=flowcell, lane_id=lane_id)
 491     LOGGER.debug("guess_library_from_model: %s", lane_body)
 492     lanes = []
 493     tries = 3
 494     while len(lanes) == 0 and tries > 0:
 495         tries -= 1
 496         lane_query = RDF.SPARQLQuery(lane_body)
 497         lanes = [ l for l in lane_query.execute(model)]
 498         if len(lanes) > 1:
 499             # CONFUSED!
 500             errmsg = "Too many libraries for flowcell {flowcell} "\
 501                      "lane {lane} = {count}"
 502             LOGGER.error(errmsg.format(flowcell=flowcell,
 503                                        lane=lane_id,
 504                                        count=len(lanes)))
 505             return None
 506         elif len(lanes) == 1:
 507             # success
 508             return lanes[0]['library']
 509         else:
 510             # try grabbing data
 511             model.load(flowcellNode.uri, name="rdfa")