################################################################################# # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc. # # All rights reserved. # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # * Redistributions of source code must retain the above copyright # notice, this list of conditions and the following disclaimer. # * Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and/or other materials provided with the distribution. # * Neither the name of Pacific Biosciences nor the names of its # contributors may be used to endorse or promote products derived from # this software without specific prior written permission. # # NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY # THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS # CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A # PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR # ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, # EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, # PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR # BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER # IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. ################################################################################# # Authors: David Alexander, Jim Bullard __all__ = [ "BasH5Reader" , "BaxH5Reader" , "BasH5Collection" ] import h5py, numpy as np, os.path as op from bisect import bisect_left, bisect_right from operator import getitem from itertools import groupby from collections import OrderedDict from pbcore.io.FofnIO import readFofn from pbcore.chemistry import (decodeTriple, tripleFromMetadataXML, ChemistryLookupError) from pbcore.model import ExtraBaseRegionsMixin, HQ_REGION from ._utils import arrayFromDataset, CommonEqualityMixin # ZMW hole Types SEQUENCING_ZMW = 0 # This seems to be the magic incantation to get a RecArray that can be # indexed to yield a record that can then be accessed using dot # notation. def toRecArray(dtype, arr): return np.rec.array(arr, dtype=dtype).flatten() REGION_TABLE_DTYPE = [("holeNumber", np.int32), ("regionType", np.int32), ("regionStart", np.int32), ("regionEnd", np.int32), ("regionScore", np.int32) ] def _makeQvAccessor(featureName): def f(self): return self.qv(featureName) return f class Zmw(CommonEqualityMixin, ExtraBaseRegionsMixin): """ A Zmw represents all data from a ZMW (zero-mode waveguide) hole within a bas.h5 movie file. Accessor methods provide convenient access to the read (or subreads), and to the region table entries for this hole. """ __slots__ = [ "baxH5", "holeNumber", "index"] def __init__(self, baxH5, holeNumber): self.baxH5 = baxH5 self.holeNumber = holeNumber self.index = self.baxH5._holeNumberToIndex[holeNumber] @property def regionTable(self): if self.holeNumber in self.baxH5._regionTableIndex: startRow, endRow = self.baxH5._regionTableIndex[self.holeNumber] return self.baxH5.regionTable[startRow:endRow] else: # Broken region table---primary pipeline bug (see bugs # 23585, 25273). Work around this by returning a fake # regiontable consisting of an empty HQ region return toRecArray(REGION_TABLE_DTYPE, [ (self.holeNumber, HQ_REGION, 0, 0, 0) ]) @property def readScore(self): """ Return the "read score", a prediction of the accuracy (between 0 and 1) of the basecalls from this ZMW, from the `ReadScore` dataset in the file """ return self.zmwMetric("ReadScore") @property def productivity(self): """ Return the 'productivity' of this ZMW, which is the estimated number of polymerase reactions taking place within it. For example, a doubly-loaded ZMW would have productivity 2. """ return self.zmwMetric("Productivity") @property def hqRegionSnr(self): """ Return the SNRs, as a vector by channel. """ return self.zmwMetric("HQRegionSNR") def zmwMetric(self, name): """ Return the value of metric 'name' from the ZMW metrics. """ return self.baxH5.zmwMetric(name, self.index) def listZmwMetrics(self): """ List the available ZMW metrics for this bax.h5 file. """ return self.baxH5.listZmwMetrics() @property def numPasses(self): """ Return the number of passes (forward + back) across the SMRTbell insert, used to forming the CCS consensus. """ if not self.baxH5.hasConsensusBasecalls: raise ValueError, "No CCS reads in this file" return self.baxH5._ccsNumPasses[self.index] @property def numEvents(self): """ Total number of basecall events in the ZMW """ offsets = self.baxH5._offsetsByHole[self.holeNumber] return offsets[1] - offsets[0] # # The following calls return one or more ZmwRead objects. # def read(self, readStart=None, readEnd=None): """ Given no arguments, returns the entire (HQ-clipped) polymerase read. With readStart, readEnd arguments, returns the specified extent of the polymerase read. """ if not self.baxH5.hasRawBasecalls: raise ValueError, "No raw reads in this file" hqStart, hqEnd = self.hqRegion readStart = hqStart if readStart is None else readStart readEnd = hqEnd if readEnd is None else readEnd return ZmwRead(self.baxH5, self.holeNumber, readStart, readEnd) def readNoQC(self, readStart=None, readEnd=None): """ Given no arguments, returns the entire polymerase read, *not HQ-clipped*. With readStart, readEnd arguments, returns the specified extent of the polymerase read. .. warning:: It is not recommended that production code use this method as we make no guarantees about what happens outside of the HQ region. """ polymeraseBegin = 0 polymeraseEnd = self.numEvents readStart = polymeraseBegin if readStart is None else readStart readEnd = polymeraseEnd if readEnd is None else readEnd return ZmwRead(self.baxH5, self.holeNumber, readStart, readEnd) @property def ccsRead(self): if not self.baxH5.hasConsensusBasecalls: raise ValueError, "No CCS reads in this file" baseOffset = self.baxH5._ccsOffsetsByHole[self.holeNumber] if (baseOffset[1] - baseOffset[0]) <= 0: return None else: return CCSZmwRead(self.baxH5, self.holeNumber, 0, baseOffset[1] - baseOffset[0]) @property def zmwName(self): return "%s/%d" % (self.baxH5.movieName, self.holeNumber) def __repr__(self): return "" % self.zmwName class ZmwRead(CommonEqualityMixin): """ A ZmwRead represents the data features (basecalls as well as pulse features) recorded from the ZMW, delimited by readStart and readEnd. """ __slots__ = [ "baxH5", "holeNumber", "readStart", "readEnd", "offsetBegin", "offsetEnd" ] def __init__(self, baxH5, holeNumber, readStart, readEnd): self.baxH5 = baxH5 self.holeNumber = holeNumber self.readStart = readStart self.readEnd = readEnd zmwOffsetBegin, zmwOffsetEnd = self._getOffsets()[self.holeNumber] self.offsetBegin = zmwOffsetBegin + self.readStart self.offsetEnd = zmwOffsetBegin + self.readEnd if not (zmwOffsetBegin <= self.offsetBegin <= self.offsetEnd <= zmwOffsetEnd): raise IndexError, "Invalid slice of Zmw!" def _getBasecallsGroup(self): return self.baxH5._basecallsGroup def _getOffsets(self): return self.baxH5._offsetsByHole @property def zmw(self): return self.baxH5[self.holeNumber] @property def readName(self): return "%s/%d_%d" % (self.zmw.zmwName, self.readStart, self.readEnd) def __repr__(self): return "<%s: %s>" % (self.__class__.__name__, self.readName) def __len__(self): return self.readEnd - self.readStart def basecalls(self): return arrayFromDataset(self._getBasecallsGroup()["Basecall"], self.offsetBegin, self.offsetEnd).tostring() def qv(self, qvName): return arrayFromDataset(self._getBasecallsGroup()[qvName], self.offsetBegin, self.offsetEnd) PreBaseFrames = _makeQvAccessor("PreBaseFrames") IPD = _makeQvAccessor("PreBaseFrames") WidthInFrames = _makeQvAccessor("WidthInFrames") PulseWidth = _makeQvAccessor("WidthInFrames") QualityValue = _makeQvAccessor("QualityValue") InsertionQV = _makeQvAccessor("InsertionQV") DeletionQV = _makeQvAccessor("DeletionQV") DeletionTag = _makeQvAccessor("DeletionTag") MergeQV = _makeQvAccessor("MergeQV") SubstitutionQV = _makeQvAccessor("SubstitutionQV") SubstitutionTag = _makeQvAccessor("SubstitutionTag") PulseIndex = _makeQvAccessor("PulseIndex") class CCSZmwRead(ZmwRead): """ Class providing access to the CCS (circular consensus sequencing) data calculated for a ZMW. """ def _getBasecallsGroup(self): return self.baxH5._ccsBasecallsGroup def _getOffsets(self): return self.baxH5._ccsOffsetsByHole @property def readName(self): return "%s/ccs" % self.zmw.zmwName def _makeOffsetsDataStructure(h5Group): numEvent = h5Group["ZMW/NumEvent"].value holeNumber = h5Group["ZMW/HoleNumber"].value endOffset = np.cumsum(numEvent, dtype=np.uint32) singleZero = np.array([0], dtype=np.uint32) beginOffset = np.hstack((singleZero, endOffset[0:-1])) offsets = zip(beginOffset, endOffset) return dict(zip(holeNumber, offsets)) def _makeRegionTableIndex(regionTableHoleNumbers): # returns a dict: holeNumber -> (startRow, endRow) diffs = np.ediff1d(regionTableHoleNumbers, to_begin=[1], to_end=[1]) changepoints = np.flatnonzero(diffs) startsAndEnds = zip(changepoints[:-1], changepoints[1:]) return dict(zip(np.unique(regionTableHoleNumbers), startsAndEnds)) class BaxH5Reader(object): """ The `BaxH5Reader` class provides access to bax.h5 file and single-part bas.h5 files. """ def __init__(self, filename, regionH5Filename=None): try: self.filename = op.abspath(op.expanduser(filename)) self.file = h5py.File(self.filename, "r") except IOError: raise IOError, ("Invalid or nonexistent bax/bas file %s" % filename) # # Raw base calls? # if "/PulseData/BaseCalls/Basecall" in self.file: self._basecallsGroup = self.file["/PulseData/BaseCalls"] self._offsetsByHole = _makeOffsetsDataStructure(self._basecallsGroup) self.hasRawBasecalls = True else: self.hasRawBasecalls = False # # CCS base calls? # if "/PulseData/ConsensusBaseCalls" in self.file: self._ccsBasecallsGroup = self.file["/PulseData/ConsensusBaseCalls"] self._ccsOffsetsByHole = _makeOffsetsDataStructure(self._ccsBasecallsGroup) self._ccsNumPasses = self._ccsBasecallsGroup["Passes/NumPasses"] self.hasConsensusBasecalls = True else: self.hasConsensusBasecalls = False self._mainBasecallsGroup = self._basecallsGroup if self.hasRawBasecalls \ else self._ccsBasecallsGroup if regionH5Filename is None: # load region information from the bas/bax file self._loadRegions(self.file) else: # load region information from a separate region file self.loadExternalRegions(regionH5Filename) # Create a variable to store the chemistry information self._sequencingChemistry = None # # ZMW metric cache -- probably want to move prod and readScore # here. # self.__metricCache = {} def _loadRegions(self, fh): """ Loads region table information from the given file handle and applies it to the ZMW data. """ holeNumbers = self._mainBasecallsGroup["ZMW/HoleNumber"].value self._holeNumberToIndex = dict(zip(holeNumbers, range(len(holeNumbers)))) # # Region table # self.regionTable = toRecArray(REGION_TABLE_DTYPE, fh["/PulseData/Regions"].value) self._regionTableIndex = _makeRegionTableIndex(self.regionTable.holeNumber) isHqRegion = self.regionTable.regionType == HQ_REGION hqRegions = self.regionTable[isHqRegion] if len(hqRegions) != len(holeNumbers): # Bug 23585: pre-2.1 primary had a bug where a bas file # could get a broken region table, lacking an HQ region # entry for a ZMW. This happened fairly rarely, mostly on # very long traces. Workaround here is to rebuild HQ # regions table with empty HQ region entries for those # ZMWs. hqRegions_ = toRecArray(REGION_TABLE_DTYPE, np.zeros(shape=len(holeNumbers), dtype=REGION_TABLE_DTYPE)) hqRegions_.holeNumber = holeNumbers for record in hqRegions: hn = record.holeNumber hqRegions_[self._holeNumberToIndex[hn]] = record hqRegions = hqRegions_ hqRegionLength = hqRegions.regionEnd - hqRegions.regionStart holeStatus = self._mainBasecallsGroup["ZMW/HoleStatus"].value # # Sequencing ZMWs - Note: this differs from Primary's # definition. To obtain those values, one would use the # `allSequencingZmws` property. # self._sequencingZmws = \ holeNumbers[(holeStatus == SEQUENCING_ZMW) & (self._mainBasecallsGroup["ZMW/NumEvent"].value > 0) & (hqRegionLength > 0)] self._allSequencingZmws = holeNumbers[holeStatus == SEQUENCING_ZMW] def loadExternalRegions(self, regionH5Filename): """ Loads regions defined in the given file, overriding those found in the bas/bax file. """ try: fh = h5py.File(op.abspath(op.expanduser(regionH5Filename)), "r") except IOError: raise IOError, ("Invalid or nonexistent file %s" % regionH5Filename) self._loadRegions(fh) fh.close() # A sanity check that the given region table provides information for # hole numbers contain in this base file. baxHoleNumbers = self._mainBasecallsGroup["ZMW/HoleNumber"].value rgnHoleNumbers = self.regionTable.holeNumber if not np.in1d(rgnHoleNumbers, baxHoleNumbers).all(): msg = "Region file (%s) does not contain the same hole numbers as " \ "bas/bax file (%s)" raise IOError, (msg % (regionH5Filename, self.filename)) @property def sequencingZmws(self): """ A list of the hole numbers that produced useable sequence data. Specifically, this means ZMWs that have an HQ region. """ return self._sequencingZmws @property def allSequencingZmws(self): """ A list of the hole numbers that are capable of producing sequencing data. This differs from the `sequencingZmws` in that zmws are not filtered according to their HQ status. This number is fixed per chip, whereas the `sequencingZmws` depends on things such as loading. """ return self._allSequencingZmws def __getitem__(self, holeNumber): return Zmw(self, holeNumber) # # Iterators over Zmws, ZmwReads # def __iter__(self): for holeNumber in self.sequencingZmws: yield self[holeNumber] def reads(self): if self.hasRawBasecalls: for zmw in self: yield zmw.read() def subreads(self): if self.hasRawBasecalls: for zmw in self: for subread in zmw.subreads: yield subread def ccsReads(self): if self.hasConsensusBasecalls: for zmw in self: if zmw.ccsRead is not None: yield zmw.ccsRead # ------------------------------ @property def movieName(self): movieNameAttr = self.file["/ScanData/RunInfo"].attrs["MovieName"] # In old bas.h5 files, attributes of ScanData/RunInfo are stored as # strings in arrays of length one. if (isinstance(movieNameAttr, (np.ndarray, list)) and len(movieNameAttr) == 1): movieNameString = movieNameAttr[0] else: movieNameString = movieNameAttr if not isinstance(movieNameString, basestring): raise TypeError("Unsupported movieName {m} of type {t}." .format(m=movieNameString, t=type(movieNameString))) return movieNameString @property def _chemistryBarcodeTripleInFile(self): """ The chemistry barcode triple consists of (BindingKit, SequencingKit, SoftwareVersion) and is written on the instrument to the bax file as of primary version 2.1. Prior to that, it was only written in the metadata.xml. """ try: bindingKit = self.file["/ScanData/RunInfo"].attrs["BindingKit"] sequencingKit = self.file["/ScanData/RunInfo"].attrs["SequencingKit"] # version string in bas file looks like "2.1.1.1.x", we have to extract # the "2.1" tmp = self.file["/PulseData/BaseCalls"].attrs["ChangeListID"] swVersion= ".".join(tmp.split(".")[0:2]) return (bindingKit, sequencingKit, swVersion) except: return None @property def _chemistryBarcodeTripleFromMetadataXML(self): try: movieName = self.movieName _up = op.dirname(op.dirname(self.filename)) metadataLocation = op.join(_up, movieName + ".metadata.xml") triple = tripleFromMetadataXML(metadataLocation) return triple except ChemistryLookupError: return None @property def chemistryBarcodeTriple(self): triple = self._chemistryBarcodeTripleInFile or self._chemistryBarcodeTripleFromMetadataXML if triple: return triple else: raise ChemistryLookupError, "Could not find chemistry barcodes in file or companion metadata.xml" @property def sequencingChemistry(self): """ Find the name of the chemistry by consulting, in order of preference: 1) Barcode triple in file 2) "SequencingChemistry" attr in file (chemistry override) 3) metadata.xml companion file """ if self._sequencingChemistry is None: triple = self._chemistryBarcodeTripleInFile if triple is not None: self._sequencingChemistry = decodeTriple(*triple) elif "SequencingChemistry" in self.file["/ScanData/RunInfo"].attrs: self._sequencingChemistry = self.file["/ScanData/RunInfo"].attrs["SequencingChemistry"] else: tripleFromXML = self._chemistryBarcodeTripleFromMetadataXML if tripleFromXML is not None: self._sequencingChemistry = decodeTriple(*tripleFromXML) else: raise ChemistryLookupError, "Chemistry information could not be found for this file" return self._sequencingChemistry def __len__(self): return len(self.sequencingZmws) def close(self): if hasattr(self, "file") and self.file is not None: self.file.close() self.file = None def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): self.close() def listZmwMetrics(self): return self._basecallsGroup["ZMWMetrics"].keys() def zmwMetric(self, name, index): # we are going to cache these lazily because it is very likely # that if one ZMW asked for the metric others aren't far # behind. if name not in self.__metricCache: k = "/".join(("ZMWMetrics", name)) self.__metricCache[name] = self._mainBasecallsGroup[k].value v = self.__metricCache[name] if len(v.shape) > 1: return v[index,] else: return v[index] class BasH5Reader(object): """ .. testsetup:: * from pbcore.io import BasH5Reader from pbcore import data filename = data.getBasH5s()[0] b = BasH5Reader(filename) zmw8 = b[8] The `BasH5Reader` provides access to the basecall and pulse metric data encoded in PacBio bas.h5 files. To access data using a `BasH5Reader`, the standard idiom is: 1. Index into the `BasH5Reader` using the ZMW hole number to get a `Zmw` object:: >>> b >>> zmw8 = b[8] >>> zmw8 2. Extract `ZmwRead` objects from the `Zmw` object by: - Using the `.subreads` property to extract the subreads, which are the subintervals of the raw read corresponding to the SMRTbell insert:: >>> subreads = zmw8.subreads >>> print subreads [, , , , ] - For CCS bas files, using the `.ccsRead` property to extract the CCS (consensus) read, which is a consensus sequence precomputed from the subreads. Older bas files, from when CCS was computed on the instrument, may contain both CCS- and sub- reads. >>> zmw8.ccsRead - Use the `.read()` method to get the full raw read, or `.read(start, end)` to extract a custom subinterval. >>> zmw8.read() >>> zmw8.read(3390, 3400) 3. With a `ZmwRead` object in hand, extract the desired basecalls and pulse metrics:: >>> subreads[0].readName "m110818_075520_42141_c100129202555500000315043109121112_s1_p0/8/3381_3881" >>> subreads[0].basecalls() "AGCCCCGTCGAGAACATACAGGTGGCCAATTTCACAGCCTCTTGCCTGGGCGATCCCGAACATCGCACCGGA..." >>> subreads[0].InsertionQV() array([12, 12, 10, 2, 7, 14, 13, 18, 15, 16, 16, 15, 10, 12, 3, 14, ...]) Note that not every ZMW on a chip produces usable sequencing data. The `BasH5Reader` has a property `sequencingZmws` is a list of the hole numbers where usable sequence was recorded. Iteration over the `BasH5Reader` object allows you to iterate over the `Zmw` objects providing usable sequence. """ def __init__(self, *args): assert len(args) > 0 if len(args) == 1: filename = args[0] try: self.filename = op.abspath(op.expanduser(filename)) self.file = h5py.File(self.filename, "r") except IOError: raise IOError, ("Invalid or nonexistent bas/bax file %s" % filename) # Is this a multi-part or single-part? if self.file.get("MultiPart"): directory = op.dirname(self.filename) self._parts = [ BaxH5Reader(op.join(directory, fn)) for fn in self.file["/MultiPart/Parts"] ] self._holeLookupDict = dict(zip(self.file["/MultiPart/HoleLookup"][:,0], self.file["/MultiPart/HoleLookup"][:,1])) self._holeLookup = self._holeLookupDict.get else: self._parts = [ BaxH5Reader(self.filename) ] self._holeLookup = (lambda holeNumber: 1) else: partFilenames = args self.filename = None self.file = None self._parts = [ BaxH5Reader(fn) for fn in partFilenames ] holeLookupDict = { hn : (i + 1) for i in xrange(len(self._parts)) for hn in self._parts[i]._holeNumberToIndex } self._holeLookup = lambda hn: holeLookupDict[hn] self._sequencingZmws = np.concatenate([ part.sequencingZmws for part in self._parts ]) @property def parts(self): return self._parts @property def sequencingZmws(self): return self._sequencingZmws @property def allSequencingZmws(self): return np.concatenate([ part.allSequencingZmws for part in self._parts ]) @property def hasConsensusBasecalls(self): return all(part.hasConsensusBasecalls for part in self._parts) @property def hasRawBasecalls(self): return all(part.hasRawBasecalls for part in self._parts) # # Iterators # def __iter__(self): """ Iterate over ZMWs """ for holeNumber in self.sequencingZmws: yield self[holeNumber] def reads(self): for part in self._parts: for read in part.reads(): yield read def subreads(self): for part in self._parts: for subread in part.subreads(): yield subread def ccsReads(self): for part in self._parts: for ccsRead in part.ccsReads(): yield ccsRead # ---------- def __len__(self): return len(self.sequencingZmws) def _getitemScalar(self, holeNumber): part = self.parts[self._holeLookup(holeNumber)-1] return part[holeNumber] def __getitem__(self, holeNumbers): if (isinstance(holeNumbers, int) or issubclass(type(holeNumbers), np.integer)): return self._getitemScalar(holeNumbers) elif isinstance(holeNumbers, slice): return [ self._getitemScalar(r) for r in xrange(*holeNumbers.indices(len(self)))] elif isinstance(holeNumbers, list) or isinstance(holeNumbers, np.ndarray): if len(holeNumbers) == 0: return [] else: entryType = type(holeNumbers[0]) if entryType == int or issubclass(entryType, np.integer): return [ self._getitemScalar(r) for r in holeNumbers ] elif entryType == bool or issubclass(entryType, np.bool_): return [ self._getitemScalar(r) for r in np.flatnonzero(holeNumbers) ] raise TypeError, "Invalid type for BasH5Reader slicing" @property def movieName(self): return self._parts[0].movieName @property def chemistryBarcodeTriple(self): return self._parts[0].chemistryBarcodeTriple @property def sequencingChemistry(self): return self._parts[0].sequencingChemistry def __len__(self): return len(self.sequencingZmws) def close(self): if hasattr(self, "file") and self.file is not None: self.file.close() self.file = None for part in self.parts: part.close() def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): self.close() def __iter__(self): for holeNumber in self.sequencingZmws: yield self[holeNumber] def __repr__(self): return "" % self.movieName # Make cursor classes available Zmw = Zmw ZmwRead = ZmwRead CCSZmwRead = CCSZmwRead def sniffMovieName(basFilename): # The clean way to do this is the get the moviename attribute from # the file, but unfortunately that approach is unusable slow. # Here we assume that the filename follows the standard PacBio # naming convention. movieName = op.basename(basFilename).split(".")[0] return movieName class BasH5Collection(object): """ Class representing a collection of base call (bas/bax) files. Can be initialized from a list of bas/bax files, or an input.fofn file containing a list of bas/bax files """ def __init__(self, *args): # # Implementation notes: find all the bas/bax files, and group # them together by movieName # basFilenames = [] for arg in args: if arg.endswith(".fofn"): for fn in readFofn(arg): basFilenames.append(fn) else: basFilenames.append(arg) movieNames = map(sniffMovieName, basFilenames) movieNamesAndFiles = sorted(zip(movieNames, basFilenames)) self.readers = OrderedDict( [ (k , BasH5Reader(*[val[1] for val in v])) for k, v in groupby(movieNamesAndFiles, lambda t: t[0]) ]) @property def movieNames(self): return self.readers.keys() def __getitem__(self, key): """ Slice by movie name, zmw name, or zmw range name, using standard PacBio naming conventions. Examples: - ["m110818_..._s1_p0"] -> BasH5Reader - ["m110818_..._s1_p0/24480"] -> Zmw - ["m110818_..._s1_p0/24480/20_67"] -> ZmwRead - ["m110818_..._s1_p0/24480/ccs"] -> CCSZmwRead """ indices = key.rstrip("/").split("/") if len(indices) < 1: raise KeyError("Invalid slice of BasH5Collection") if len(indices) >= 1: result = self.readers[indices[0]] if len(indices) >= 2: result = result[int(indices[1])] if len(indices) >= 3: if indices[2] == "ccs": result = result.ccsRead else: start, end = map(int, indices[2].split("_")) result = result.read(start, end) return result # # Iterators over Zmw, ZmwRead objects # def __iter__(self): for reader in self.readers.values(): for zmw in reader: yield zmw def reads(self): for reader in self.readers.values(): for read in reader.reads(): yield read def subreads(self): for reader in self.readers.values(): for read in reader.subreads(): yield read def ccsReads(self): for reader in self.readers.values(): for read in reader.ccsReads(): yield read