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      stripNamespace, 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         fileNode = RDF.Node(RDF.Uri('file://' + os.path.abspath(self.path)))
 165         add(model, fileNode, rdfNS['type'], libNS['raw_file'])
 166         add_lit(model, fileNode, libNS['flowcell_id'], self.flowcell)
 167         add_lit(model, fileNode, libNS['lane_number'], self.lane)
 168         if self.read is not None:
 169             add_lit(model, fileNode, libNS['read'], self.read)
 170         else:
 171             add_lit(model, fileNode, libNS['read'], '')
 172
 173         add_lit(model, fileNode, libNS['library_id'], self.project)
 174         add_lit(model, fileNode, libNS['multiplex_index'], self.index)
 175         add_lit(model, fileNode, libNS['split_id'], self.split)
 176         add_lit(model, fileNode, libNS['cycle'], self.cycle)
 177         add_lit(model, fileNode, libNS['passed_filter'], self.pf)
 178         add(model, fileNode, rdfNS['type'], libNS[self.filetype])
 179
 180         if base_url is not None:
 181             flowcell = RDF.Node(RDF.Uri("{base}/flowcell/{flowcell}/".format(
 182                 base=base_url,
 183                 flowcell=self.flowcell)))
 184             add(model, fileNode, libNS['flowcell'], flowcell)
 185             if self.project is not None:
 186                 library = RDF.Node(RDF.Uri("{base}/library/{library}".format(
 187                     base=base_url,
 188                     library=self.project)))
 189                 add(model, fileNode, libNS['library'], library)
 190
 191
 192     @classmethod
 193     def load_from_model(cls, model, seq_id):
 194         def get(s, p):
 195             values = []
 196             stmts = model.find_statements(RDF.Statement(s, p, None))
 197             for s in stmts:
 198                 obj = s.object
 199                 if not obj.is_resource():
 200                     values.append(fromTypedNode(obj))
 201                 else:
 202                     values.append(obj)
 203             return values
 204         def get_one(s, p):
 205             values = get(s, p)
 206             if len(values) > 1:
 207                 errmsg = u"To many values for %s %s"
 208                 raise ValueError(errmsg % (unicode(s), unicode(p)))
 209             elif len(values) == 1:
 210                 return values[0]
 211             else:
 212                 return None
 213
 214         if not isinstance(seq_id, RDF.Node):
 215             seq_id = RDF.Node(RDF.Uri(seq_id))
 216         seqTypesStmt = RDF.Statement(seq_id, rdfNS['type'], None)
 217         seqTypes = model.find_statements(seqTypesStmt)
 218         isSequenceFile = False
 219         for s in seqTypes:
 220             if s.object == libNS['raw_file']:
 221                 isSequenceFile = True
 222             else:
 223                 seq_type = stripNamespace(libNS, s.object)
 224
 225         if not isSequenceFile:
 226             raise KeyError(u"%s not found" % (unicode(seq_id),))
 227
 228         path = urlparse(str(seq_id.uri)).path
 229         flowcellNode = get_one(seq_id, libNS['flowcell'])
 230         flowcell = get_one(seq_id, libNS['flowcell_id'])
 231         lane = get_one(seq_id, libNS['lane_number'])
 232         read = get_one(seq_id, libNS['read'])
 233
 234         obj = cls(seq_type, path, flowcell, lane)
 235         obj.read = read if read != '' else None
 236         obj.project = get_one(seq_id, libNS['library_id'])
 237         obj.index = get_one(seq_id, libNS['multiplex_index'])
 238         obj.split = get_one(seq_id, libNS['split_id'])
 239         obj.cycle = get_one(seq_id, libNS['cycle'] )
 240         obj.pf = get_one(seq_id, libNS['passed_filter'])
 241         obj.libraryNode = get_one(seq_id, libNS['library'])
 242         return obj
 243
 244
 245 def get_flowcell_cycle(path):
 246     """
 247     Extract flowcell, cycle from pathname
 248     """
 249     path = os.path.normpath(path)
 250     project = None
 251     rest, tail = os.path.split(path)
 252     if tail.startswith('Project_'):
 253         # we're in a multiplexed sample
 254         project = tail
 255         rest, cycle = os.path.split(rest)
 256     else:
 257         cycle = tail
 258
 259     rest, flowcell = os.path.split(rest)
 260     cycle_match = re.match("C(?P<start>[0-9]+)-(?P<stop>[0-9]+)", cycle)
 261     if cycle_match is None:
 262         raise ValueError(
 263             "Expected .../flowcell/cycle/ directory structure in %s" % \
 264             (path,))
 265     start = cycle_match.group('start')
 266     if start is not None:
 267         start = int(start)
 268     stop = cycle_match.group('stop')
 269     if stop is not None:
 270         stop = int(stop)
 271
 272     return FlowcellPath(flowcell, start, stop, project)
 273
 274 def parse_srf(path, filename):
 275     flowcell_dir, start, stop, project = get_flowcell_cycle(path)
 276     basename, ext = os.path.splitext(filename)
 277     records = basename.split('_')
 278     flowcell = records[4]
 279     lane = int(records[5][0])
 280     fullpath = os.path.join(path, filename)
 281
 282     if flowcell_dir != flowcell:
 283         LOGGER.warn("flowcell %s found in wrong directory %s" % \
 284                          (flowcell, path))
 285
 286     return SequenceFile('srf', fullpath, flowcell, lane, cycle=stop)
 287
 288 def parse_qseq(path, filename):
 289     flowcell_dir, start, stop, project = get_flowcell_cycle(path)
 290     basename, ext = os.path.splitext(filename)
 291     records = basename.split('_')
 292     fullpath = os.path.join(path, filename)
 293     flowcell = records[4]
 294     lane = int(records[5][1])
 295     read = int(records[6][1])
 296
 297     if flowcell_dir != flowcell:
 298         LOGGER.warn("flowcell %s found in wrong directory %s" % \
 299                          (flowcell, path))
 300
 301     return SequenceFile('qseq', fullpath, flowcell, lane, read, cycle=stop)
 302
 303 def parse_fastq(path, filename):
 304     """Parse fastq names
 305     """
 306     flowcell_dir, start, stop, project = get_flowcell_cycle(path)
 307     basename = re.sub('\.fastq(\.gz|\.bz2)?$', '', filename)
 308     records = basename.split('_')
 309     fullpath = os.path.join(path, filename)
 310     if project is not None:
 311         # demultiplexed sample!
 312         flowcell = flowcell_dir
 313         lane = int(records[2][-1])
 314         read = int(records[3][-1])
 315         pf = True # as I understand it hiseq runs toss the ones that fail filter
 316         index = records[1]
 317         project_id = records[0]
 318         split = records[4]
 319         sequence_type = 'split_fastq'
 320     else:
 321         flowcell = records[4]
 322         lane = int(records[5][1])
 323         read = int(records[6][1])
 324         pf = parse_fastq_pf_flag(records)
 325         index = None
 326         project_id = None
 327         split = None
 328         sequence_type = 'fastq'
 329
 330     if flowcell_dir != flowcell:
 331         LOGGER.warn("flowcell %s found in wrong directory %s" % \
 332                          (flowcell, path))
 333
 334     return SequenceFile(sequence_type, fullpath, flowcell, lane, read,
 335                         pf=pf,
 336                         cycle=stop,
 337                         project=project_id,
 338                         index=index,
 339                         split=split)
 340
 341 def parse_fastq_pf_flag(records):
 342     """Take a fastq filename split on _ and look for the pass-filter flag
 343     """
 344     if len(records) < 8:
 345         pf = None
 346     else:
 347         fastq_type = records[-1].lower()
 348         if fastq_type.startswith('pass'):
 349             pf = True
 350         elif fastq_type.startswith('nopass'):
 351             pf = False
 352         elif fastq_type.startswith('all'):
 353             pf = None
 354         else:
 355             raise ValueError("Unrecognized fastq name: %s" % (
 356                 "_".join(records),))
 357
 358     return pf
 359
 360 def parse_eland(path, filename, eland_match=None):
 361     if eland_match is None:
 362         eland_match = eland_re.match(filename)
 363     fullpath = os.path.join(path, filename)
 364     flowcell, start, stop, project = get_flowcell_cycle(path)
 365     if eland_match.group('lane'):
 366         lane = int(eland_match.group('lane'))
 367     else:
 368         lane = None
 369     if eland_match.group('read'):
 370         read = int(eland_match.group('read'))
 371     else:
 372         read = None
 373     return SequenceFile('eland', fullpath, flowcell, lane, read, cycle=stop)
 374
 375 def scan_for_sequences(dirs):
 376     """
 377     Scan through a list of directories for sequence like files
 378     """
 379     sequences = []
 380     if type(dirs) in types.StringTypes:
 381         raise ValueError("You probably want a list or set, not a string")
 382
 383     for d in dirs:
 384         LOGGER.info("Scanning %s for sequences" % (d,))
 385         if not os.path.exists(d):
 386             LOGGER.warn("Flowcell directory %s does not exist" % (d,))
 387             continue
 388
 389         for path, dirname, filenames in os.walk(d):
 390             for f in filenames:
 391                 seq = None
 392                 # find sequence files
 393                 if f.endswith('.md5'):
 394                     continue
 395                 elif f.endswith('.srf') or f.endswith('.srf.bz2'):
 396                     seq = parse_srf(path, f)
 397                 elif qseq_re.match(f):
 398                     seq = parse_qseq(path, f)
 399                 elif f.endswith('.fastq') or \
 400                      f.endswith('.fastq.bz2') or \
 401                      f.endswith('.fastq.gz'):
 402                     seq = parse_fastq(path, f)
 403                 eland_match = eland_re.match(f)
 404                 if eland_match:
 405                     if f.endswith('.md5'):
 406                         continue
 407                     seq = parse_eland(path, f, eland_match)
 408                 if seq:
 409                     sequences.append(seq)
 410                     LOGGER.debug("Found sequence at %s" % (f,))
 411
 412     return sequences
 413
 414
 415 def update_model_sequence_library(model, base_url):
 416     """Find sequence objects and add library information if its missing
 417     """
 418     file_body = """
 419     prefix libNS: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 420     select ?filenode ?flowcell_id ?lane_id ?library_id ?flowcell ?library
 421     where {
 422        ?filenode a libNS:raw_file ;
 423                  libNS:flowcell_id ?flowcell_id ;
 424                  libNS:lane_number ?lane_id .
 425        OPTIONAL { ?filenode libNS:flowcell ?flowcell . }
 426        OPTIONAL { ?filenode libNS:library ?library .}
 427        OPTIONAL { ?filenode libNS:library_id ?library_id .}
 428     }
 429     """
 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         lane_id = fromTypedNode(f['lane_id'])
 438         if f['flowcell'] is None:
 439             flowcell = flowcellNS[str(f['flowcell_id'])+'/']
 440             model.add_statement(
 441                 RDF.Statement(filenode, libNS['flowcell'], flowcell))
 442         else:
 443             flowcell = f['flowcell']
 444
 445         if f['library'] is None:
 446             if f['library_id'] is not None:
 447                 library = libraryNS[str(f['library_id']) + '/']
 448             else:
 449                 library = guess_library_from_model(model, base_url,
 450                                                    flowcell,
 451                                                    lane_id)
 452                 library_id = toTypedNode(simplify_uri(library))
 453                 model.add_statement(
 454                     RDF.Statement(filenode, libNS['library_id'], library_id))
 455             if library is not None:
 456                 model.add_statement(
 457                     RDF.Statement(filenode, libNS['library'], library))
 458
 459
 460 def guess_library_from_model(model, base_url, flowcell, lane_id):
 461     """Attempt to find library URI
 462     """
 463     flowcellNode = RDF.Node(flowcell)
 464     flowcell = str(flowcell.uri)
 465     lane_body = """
 466     prefix libNS: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 467     prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 468     prefix xsd: <http://www.w3.org/2001/XMLSchema#>
 469
 470     select ?library ?lane
 471     where {{
 472       <{flowcell}> libNS:has_lane ?lane ;
 473                    a libNS:illumina_flowcell .
 474       ?lane libNS:lane_number {lane_id} ;
 475             libNS:library ?library .
 476     }}
 477     """
 478     lane_body = lane_body.format(flowcell=flowcell, lane_id=lane_id)
 479     lanes = []
 480     tries = 3
 481     while len(lanes) == 0 and tries > 0:
 482         tries -= 1
 483         lane_query = RDF.SPARQLQuery(lane_body)
 484         lanes = [ l for l in lane_query.execute(model)]
 485         if len(lanes) > 1:
 486             # CONFUSED!
 487             errmsg = "Too many libraries for flowcell {flowcell} "\
 488                      "lane {lane} = {count}"
 489             LOGGER.error(errmsg.format(flowcell=flowcell,
 490                                        lane=lane_id,
 491                                        count=len(lanes)))
 492             return None
 493         elif len(lanes) == 1:
 494             # success
 495             return lanes[0]['library']
 496         else:
 497             # try grabbing data
 498             model.load(flowcellNode.uri, name="rdfa")
 499
 500