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
  10 LOGGER = logging.getLogger(__name__)
  11
  12 eland_re = re.compile('s_(?P<lane>\d)(_(?P<read>\d))?_eland_')
  13 raw_seq_re = re.compile('woldlab_[0-9]{6}_[^_]+_[\d]+_[\dA-Za-z]+')
  14 qseq_re = re.compile('woldlab_[0-9]{6}_[^_]+_[\d]+_[\dA-Za-z]+_l[\d]_r[\d].tar.bz2')
  15
  16 SEQUENCE_TABLE_NAME = "sequences"
  17 def create_sequence_table(cursor):
  18     """
  19     Create a SQL table to hold  SequenceFile entries
  20     """
  21     sql = """
  22 CREATE TABLE %(table)s (
  23   filetype   CHAR(8),
  24   path       TEXT,
  25   flowcell   CHAR(8),
  26   lane       INTEGER,
  27   read       INTEGER,
  28   pf         BOOLEAN,
  29   cycle      CHAR(8)
  30 );
  31 """ %( {'table': SEQUENCE_TABLE_NAME} )
  32     return cursor.execute(sql)
  33
  34 FlowcellPath = collections.namedtuple('FlowcellPath',
  35                                       'flowcell start stop project')
  36
  37 class SequenceFile(object):
  38     """
  39     Simple container class that holds the path to a sequence archive
  40     and basic descriptive information.
  41     """
  42     def __init__(self, filetype, path, flowcell, lane,
  43                  read=None,
  44                  pf=None,
  45                  cycle=None,
  46                  project=None,
  47                  index=None,
  48                  split=None):
  49         """Store various fields used in our sequence files
  50
  51         filetype is one of 'qseq', 'srf', 'fastq'
  52         path = location of file
  53         flowcell = files flowcell id
  54         lane = which lane
  55         read = which sequencer read, usually 1 or 2
  56         pf = did it pass filter
  57         cycle = cycle dir name e.g. C1-202
  58         project = projed name from HiSeq, probably library ID
  59         index = HiSeq barcode index sequence
  60         split = file fragment from HiSeq (Since one file is split into many)
  61         """
  62         self.filetype = filetype
  63         self.path = path
  64         self.flowcell = flowcell
  65         self.lane = lane
  66         self.read = read
  67         self.pf = pf
  68         self.cycle = cycle
  69         self.project = project
  70         self.index = index
  71         self.split = split
  72
  73     def __hash__(self):
  74         return hash(self.key())
  75
  76     def key(self):
  77         return (self.flowcell, self.lane, self.read, self.project, self.split)
  78
  79     def unicode(self):
  80         return unicode(self.path)
  81
  82     def __eq__(self, other):
  83         """
  84         Equality is defined if everything but the path matches
  85         """
  86         attributes = ['filetype',
  87                       'flowcell',
  88                       'lane',
  89                       'read',
  90                       'pf',
  91                       'cycle',
  92                       'project',
  93                       'index',
  94                       'split']
  95         for a in attributes:
  96             if getattr(self, a) != getattr(other, a):
  97                 return False
  98
  99         return True
 100
 101     def __repr__(self):
 102         return u"<%s %s %s %s>" % (self.filetype, self.flowcell, self.lane, self.path)
 103
 104     def make_target_name(self, root):
 105         """
 106         Create target name for where we need to link this sequence too
 107         """
 108         path, basename = os.path.split(self.path)
 109         # Because the names aren't unque we include the flowcel name
 110         # because there were different eland files for different length
 111         # analyses, we include the cycle length in the name.
 112         if self.filetype == 'eland':
 113             template = "%(flowcell)s_%(cycle)s_%(eland)s"
 114             basename = template % { 'flowcell': self.flowcell,
 115                                     'cycle': self.cycle,
 116                                     'eland': basename }
 117         # else:
 118         # all the other file types have names that include flowcell/lane
 119         # information and thus are unique so we don't have to do anything
 120         return os.path.join(root, basename)
 121
 122     def save(self, cursor):
 123         """
 124         Add this entry to a DB2.0 database.
 125         """
 126         #FIXME: NEEDS SQL ESCAPING
 127         header_macro = {'table': SEQUENCE_TABLE_NAME }
 128         sql_header = "insert into %(table)s (" % header_macro
 129         sql_columns = ['filetype','path','flowcell','lane']
 130         sql_middle = ") values ("
 131         sql_values = [self.filetype, self.path, self.flowcell, self.lane]
 132         sql_footer = ");"
 133         for name in ['read', 'pf', 'cycle']:
 134             value = getattr(self, name)
 135             if value is not None:
 136                 sql_columns.append(name)
 137                 sql_values.append(value)
 138
 139         sql = " ".join([sql_header,
 140                         ", ".join(sql_columns),
 141                         sql_middle,
 142                         # note the following makes a string like ?,?,?
 143                         ",".join(["?"] * len(sql_values)),
 144                         sql_footer])
 145
 146         return cursor.execute(sql, sql_values)
 147
 148 def get_flowcell_cycle(path):
 149     """
 150     Extract flowcell, cycle from pathname
 151     """
 152     path = os.path.normpath(path)
 153     project = None
 154     rest, tail = os.path.split(path)
 155     if tail.startswith('Project_'):
 156         # we're in a multiplexed sample
 157         project = tail
 158         rest, cycle = os.path.split(rest)
 159     else:
 160         cycle = tail
 161
 162     rest, flowcell = os.path.split(rest)
 163     cycle_match = re.match("C(?P<start>[0-9]+)-(?P<stop>[0-9]+)", cycle)
 164     if cycle_match is None:
 165         raise ValueError(
 166             "Expected .../flowcell/cycle/ directory structure in %s" % \
 167             (path,))
 168     start = cycle_match.group('start')
 169     if start is not None:
 170         start = int(start)
 171     stop = cycle_match.group('stop')
 172     if stop is not None:
 173         stop = int(stop)
 174
 175     return FlowcellPath(flowcell, start, stop, project)
 176
 177 def parse_srf(path, filename):
 178     flowcell_dir, start, stop, project = get_flowcell_cycle(path)
 179     basename, ext = os.path.splitext(filename)
 180     records = basename.split('_')
 181     flowcell = records[4]
 182     lane = int(records[5][0])
 183     fullpath = os.path.join(path, filename)
 184
 185     if flowcell_dir != flowcell:
 186         LOGGER.warn("flowcell %s found in wrong directory %s" % \
 187                          (flowcell, path))
 188
 189     return SequenceFile('srf', fullpath, flowcell, lane, cycle=stop)
 190
 191 def parse_qseq(path, filename):
 192     flowcell_dir, start, stop, project = get_flowcell_cycle(path)
 193     basename, ext = os.path.splitext(filename)
 194     records = basename.split('_')
 195     fullpath = os.path.join(path, filename)
 196     flowcell = records[4]
 197     lane = int(records[5][1])
 198     read = int(records[6][1])
 199
 200     if flowcell_dir != flowcell:
 201         LOGGER.warn("flowcell %s found in wrong directory %s" % \
 202                          (flowcell, path))
 203
 204     return SequenceFile('qseq', fullpath, flowcell, lane, read, cycle=stop)
 205
 206 def parse_fastq(path, filename):
 207     """Parse fastq names
 208     """
 209     flowcell_dir, start, stop, project = get_flowcell_cycle(path)
 210     basename = re.sub('\.fastq(\.gz|\.bz2)?$', '', filename)
 211     records = basename.split('_')
 212     fullpath = os.path.join(path, filename)
 213     if project is not None:
 214         # demultiplexed sample!
 215         flowcell = flowcell_dir
 216         lane = int(records[2][-1])
 217         read = int(records[3][-1])
 218         pf = True # as I understand it hiseq runs toss the ones that fail filter
 219         index = records[1]
 220         project_id = records[0]
 221         split = records[4]
 222         sequence_type = 'split_fastq'
 223     else:
 224         flowcell = records[4]
 225         lane = int(records[5][1])
 226         read = int(records[6][1])
 227         pf = parse_fastq_pf_flag(records)
 228         index = None
 229         project_id = None
 230         split = None
 231         sequence_type = 'fastq'
 232
 233     if flowcell_dir != flowcell:
 234         LOGGER.warn("flowcell %s found in wrong directory %s" % \
 235                          (flowcell, path))
 236
 237     return SequenceFile(sequence_type, fullpath, flowcell, lane, read,
 238                         pf=pf,
 239                         cycle=stop,
 240                         project=project_id,
 241                         index=index,
 242                         split=split)
 243
 244 def parse_fastq_pf_flag(records):
 245     """Take a fastq filename split on _ and look for the pass-filter flag
 246     """
 247     if len(records) < 8:
 248         pf = None
 249     else:
 250         fastq_type = records[-1].lower()
 251         if fastq_type.startswith('pass'):
 252             pf = True
 253         elif fastq_type.startswith('nopass'):
 254             pf = False
 255         elif fastq_type.startswith('all'):
 256             pf = None
 257         else:
 258             raise ValueError("Unrecognized fastq name %s at %s" % \
 259                              (records[-1], os.path.join(path,filename)))
 260
 261     return pf
 262
 263 def parse_eland(path, filename, eland_match=None):
 264     if eland_match is None:
 265         eland_match = eland_re.match(filename)
 266     fullpath = os.path.join(path, filename)
 267     flowcell, start, stop, project = get_flowcell_cycle(path)
 268     if eland_match.group('lane'):
 269         lane = int(eland_match.group('lane'))
 270     else:
 271         lane = None
 272     if eland_match.group('read'):
 273         read = int(eland_match.group('read'))
 274     else:
 275         read = None
 276     return SequenceFile('eland', fullpath, flowcell, lane, read, cycle=stop)
 277
 278 def scan_for_sequences(dirs):
 279     """
 280     Scan through a list of directories for sequence like files
 281     """
 282     sequences = []
 283     if type(dirs) in types.StringTypes:
 284         raise ValueError("You probably want a list or set, not a string")
 285
 286     for d in dirs:
 287         LOGGER.info("Scanning %s for sequences" % (d,))
 288         if not os.path.exists(d):
 289             LOGGER.warn("Flowcell directory %s does not exist" % (d,))
 290             continue
 291
 292         for path, dirname, filenames in os.walk(d):
 293             for f in filenames:
 294                 seq = None
 295                 # find sequence files
 296                 if f.endswith('.md5'):
 297                     continue
 298                 elif f.endswith('.srf') or f.endswith('.srf.bz2'):
 299                     seq = parse_srf(path, f)
 300                 elif qseq_re.match(f):
 301                     seq = parse_qseq(path, f)
 302                 elif f.endswith('.fastq') or \
 303                      f.endswith('.fastq.bz2') or \
 304                      f.endswith('.fastq.gz'):
 305                     seq = parse_fastq(path, f)
 306                 eland_match = eland_re.match(f)
 307                 if eland_match:
 308                     if f.endswith('.md5'):
 309                         continue
 310                     seq = parse_eland(path, f, eland_match)
 311                 if seq:
 312                     sequences.append(seq)
 313                     LOGGER.debug("Found sequence at %s" % (f,))
 314
 315     return sequences