def getParms (): # use default input sys.argv[1:]
parser = optparse.OptionParser(usage='%prog [options] <bas_file>')
parser.add_option ('--linehelp', action='store_true', help='show line-specific help and exit')
parser.add_option ('--filehelp', action='store_true', help='show help for file-related parameters, and exit')
parser.add_option ('--ccs', help='directory containing ccs.h5 files for CCS reads, post-2.1.0')
parser.add_option ('--aln', help='cmp.h5 file for subread alignments')
parser.add_option ('--alnccs', help='cmp.h5 file for CCS alignments')
parser.add_option ('--score', type='int', help='minimum HQ region score (def: %default)')
parser.add_option ('--length', type='int', help='minimum HQ region length (def: %default)')
parser.add_option ('--adapter', type='int', help='expected adapter length (def: %default)')
parser.add_option ('--noadapt', action='store_true', help='do not print adapter lines (for brevity)')
parser.add_option ('--nocons', action='store_true', help='do not print consensus passes lines')
parser.set_defaults (score=DEF_SCORE_THRESHOLD,
length=DEF_HQ_LENGTH,
adapter=DEF_ADAPTER_LENGTH)
opt, args = parser.parse_args()
if opt.linehelp:
lineHelp()
if opt.filehelp:
fileHelp()
if opt.linehelp or opt.filehelp:
sys.exit()
if len(args) > 1:
logger.warning ('WARNING: alignments cmp.h5 file should now be specified with --aln keyword')
opt.aln = args.pop() # put it where it belongs
return opt, args
def findCCSFile(self):
"""Given a directory to look in, find the ccs.h5 file that contains consensus reads for this bax file."""
self._hasConsensus = False # until proven otherwise
if "PulseData/ConsensusBaseCalls" in self._top: # if this is an older bax file, in contains its own CCS data
self._consBasecalls = self._top["PulseData/ConsensusBaseCalls"]
self._consZMW = self._top["PulseData/ConsensusBaseCalls/ZMW"]
self._consPasses = self._top["PulseData/ConsensusBaseCalls/Passes"]
self._hasConsensus = True
elif self._CCSDir is not None:
CCSFilename = os.path.basename(self._filename).replace("bax", "ccs")
fqCCSFilename = os.path.join(self._CCSDir, CCSFilename)
if os.path.exists(fqCCSFilename):
self._CCSFile = h5py.File(fqCCSFilename, "r")
self._consBasecalls = self._CCSFile["PulseData/ConsensusBaseCalls"]
self._consZMW = self._CCSFile["PulseData/ConsensusBaseCalls/ZMW"]
self._consPasses = self._CCSFile["PulseData/ConsensusBaseCalls/Passes"]
self._hasConsensus = True
logger.debug("BaxFile %s found CCS file %s" % (self._shortName, fqCCSFilename))
else:
logger.warning("%s: no CCS file found corresponding to %s" % (self._shortName, self._filename))
else:
logger.info("BaxFile %s does not contain CCS data (rel 2.1.0 and later). Use --ccs" % self._shortName)
def makeTempDir (dir):
if os.path.isdir (dir):
logger.warning('WARNING: temp directory %s already exists' % dir)
else:
os.makedirs (dir)
return
def makeTempDir(dir):
if os.path.isdir(dir):
logger.warning('WARNING: temp directory %s already exists' % dir)
else:
os.makedirs(dir)
return
def getParms(): # use default input sys.argv[1:]
parser = optparse.OptionParser(usage='%prog [options] <bas_file>')
parser.add_option('--linehelp',
action='store_true',
help='show line-specific help and exit')
parser.add_option('--filehelp',
action='store_true',
help='show help for file-related parameters, and exit')
parser.add_option(
'--ccs',
help='directory containing ccs.h5 files for CCS reads, post-2.1.0')
parser.add_option('--aln', help='cmp.h5 file for subread alignments')
parser.add_option('--alnccs', help='cmp.h5 file for CCS alignments')
parser.add_option('--score',
type='int',
help='minimum HQ region score (def: %default)')
parser.add_option('--length',
type='int',
help='minimum HQ region length (def: %default)')
parser.add_option('--adapter',
type='int',
help='expected adapter length (def: %default)')
parser.add_option('--noadapt',
action='store_true',
help='do not print adapter lines (for brevity)')
parser.add_option('--nocons',
action='store_true',
help='do not print consensus passes lines')
parser.set_defaults(score=DEF_SCORE_THRESHOLD,
length=DEF_HQ_LENGTH,
adapter=DEF_ADAPTER_LENGTH)
opt, args = parser.parse_args()
if opt.linehelp:
lineHelp()
if opt.filehelp:
fileHelp()
if opt.linehelp or opt.filehelp:
sys.exit()
if len(args) > 1:
logger.warning(
'WARNING: alignments cmp.h5 file should now be specified with --aln keyword'
)
opt.aln = args.pop() # put it where it belongs
return opt, args
def getGeneFromAnnotation (opt, tranList, exonList):
'''Add to lists of transcripts and exons: annotations for gene of interest.'''
if opt.gtf == None:
return tranList, exonList
omits = [] if opt.omit is None else opt.omit.split(',') # transcripts which must not be included
if opt.annotations:
annotList = opt.annotations
else:
if opt.format == 'pickle':
annotList = anno.AnnotationList.fromPickle (opt.gtf)
elif opt.format == 'alt':
annotList = anno.AnnotationList (opt.gtf, altFormat=True)
else: # standard format
annotList = anno.AnnotationList (opt.gtf)
allGenes = annotList.getGeneDict()
if opt.gene not in allGenes:
raise RuntimeError ('gene %s is not in the annotation file' % opt.gene)
geneList = allGenes[opt.gene] # a list of Annotation objects
if len(geneList) > 1:
logger.warning('gene %s appears %d times in annotations, first occurrence plotted' \
% (opt.gene, len(geneList)))
myGene = geneList[0]
for tran in myGene.getChildren(): # tran is an Annotation object
if tran.name not in omits: # if not in ignore list
myTran = Transcript(tran.name, start=tran.start, end=tran.end, annot=True, ID=tran.ID)
if hasattr(tran, 'startcodon'):
myTran.startcodon = tran.startcodon
if hasattr(tran, 'stopcodon'):
myTran.stopcodon = tran.stopcodon
for exon in tran.getChildren(): # exon is an Annotation object
myExon = Exon(myTran, exon.name, exon.start, exon.end, exon.strand) # no Q score
if hasattr (exon, 'polyAs'):
print exon.name
myExon.polyAs = exon.polyAs
exonList.append (myExon)
myTran.exons.append(myExon)
tranList.append (myTran)
return tranList, exonList
def getGeneFromAnnotation (opt, tranList, exonList):
'''Add to lists of transcripts and exons: annotations for gene of interest.'''
if opt.gtf == None:
return tranList, exonList
omits = [] if opt.omit is None else opt.omit.split(',') # transcripts which must not be included
if opt.format == 'pickle':
annotList = anno.AnnotationList.fromPickle (opt.gtf)
elif opt.format == 'alt':
annotList = anno.AnnotationList (opt.gtf, altFormat=True)
else: # standard format
annotList = anno.AnnotationList (opt.gtf)
allGenes = annotList.getGeneDict()
if opt.gene not in allGenes:
raise RuntimeError ('gene %s is not in the annotation file' % opt.gene)
geneList = allGenes[opt.gene] # a list of Annotation objects
if len(geneList) > 1:
logger.warning('gene %s appears %d times in annotations, first occurrence plotted' \
% (opt.gene, len(geneList)))
myGene = geneList[0]
for tran in myGene.getChildren(): # tran is an Annotation object
if tran.name not in omits: # if not in ignore list
myTran = Transcript(tran.name, annot=True)
if hasattr(tran, 'startcodon'):
myTran.startcodon = tran.startcodon
if hasattr(tran, 'stopcodon'):
myTran.stopcodon = tran.stopcodon
for exon in tran.getChildren(): # exon is an Annotation object
myExon = Exon(myTran, exon.name, exon.start, exon.end, exon.strand) # no Q score
if hasattr (exon, 'polyAs'):
print exon.name
myExon.polyAs = exon.polyAs
exonList.append (myExon)
myTran.exons.append(myExon)
tranList.append (myTran)
return tranList, exonList
def getGeneFromAnnotation(opt, tranList, exonList):
# Add to lists of transcripts and exons: annotations for gene of interest.
if opt.gtf is None:
return tranList, exonList
if opt.annotations:
annotList = opt.annotations
else:
if opt.format == 'pickle':
annotList = anno.AnnotationList.fromPickle(opt.gtf)
elif opt.format == 'alt':
annotList = anno.AnnotationList(opt.gtf, altFormat=True)
else: # standard format
annotList = anno.AnnotationList(opt.gtf)
allGenes = annotList.getGeneDict()
allGenes.update({k.upper(): v for k, v in allGenes.iteritems()})
if opt.gene not in allGenes:
raise RuntimeError('gene %s is not in the annotation file' % opt.gene)
geneList = allGenes[opt.gene] # a list of Annotation objects
if len(geneList) > 1:
logger.warning(
'gene %s appears %d times in annotations, first occurrence plotted'
% (opt.gene, len(geneList)))
myGene = geneList[0]
for tran in myGene.getChildren(): # tran is an Annotation object
myTran = Transcript(tran.name,
start=tran.start,
end=tran.end,
annot=True,
ID=tran.ID,
source=(0, opt.gtf))
if hasattr(tran, 'startcodon'):
myTran.startcodon = tran.startcodon
if hasattr(tran, 'stopcodon'):
myTran.stopcodon = tran.stopcodon
for exon in tran.getChildren(): # exon is an Annotation object
myExon = Exon(myTran, exon.name, exon.start, exon.end,
exon.strand) # no Q score
if hasattr(exon, 'polyAs'):
myExon.polyAs = exon.polyAs
exonList.append(myExon)
myTran.exons.append(myExon)
tranList.append(myTran)
return tranList, exonList
def findCCSFile(self):
'''Given a directory to look in, find the ccs.h5 file that contains consensus reads for this bax file.'''
self._hasConsensus = False # until proven otherwise
if "PulseData/ConsensusBaseCalls" in self._top: # if this is an older bax file, in contains its own CCS data
self._consBasecalls = self._top["PulseData/ConsensusBaseCalls"]
self._consZMW = self._top["PulseData/ConsensusBaseCalls/ZMW"]
self._consPasses = self._top["PulseData/ConsensusBaseCalls/Passes"]
self._hasConsensus = True
elif self._CCSDir is not None:
CCSFilename = os.path.basename(self._filename).replace(
'bax', 'ccs')
fqCCSFilename = os.path.join(self._CCSDir, CCSFilename)
if os.path.exists(fqCCSFilename):
self._CCSFile = h5py.File(fqCCSFilename, 'r')
self._consBasecalls = self._CCSFile[
"PulseData/ConsensusBaseCalls"]
self._consZMW = self._CCSFile[
"PulseData/ConsensusBaseCalls/ZMW"]
self._consPasses = self._CCSFile[
"PulseData/ConsensusBaseCalls/Passes"]
self._hasConsensus = True
logger.debug('BaxFile %s found CCS file %s' %
(self._shortName, fqCCSFilename))
else:
logger.warning('%s: no CCS file found corresponding to %s' %
(self._shortName, self._filename))
else:
logger.info(
'BaxFile %s does not contain CCS data (rel 2.1.0 and later). Use --ccs'
% self._shortName)
def getParms (): # use default input sys.argv[1:]
parser = optparse.OptionParser(usage='%prog [options] <bas_file> [<cmp_file>]',
description='Print (to stdout) summary information about the contents of a bas.h5 file.')
parser.add_option ('--ccs', help='directory containing ccs.h5 files for CCS reads, post-2.1.0')
parser.add_option ('--aln', help='cmp.h5 file for subread alignments')
parser.add_option ('--score', type='int', help='Minimum HQ region score (def: %default)')
parser.add_option ('--length', type='int', help='Minimum HQ region length (def: %default)')
parser.add_option ('--insert', type='int', help='Minimum average insert length (def: %default)')
parser.set_defaults (score=DEF_SCORE_THRESHOLD,
length=DEF_HQ_LENGTH,
insert=DEF_INSERT_THRESHOLD)
opt, args = parser.parse_args()
if len(args) > 1:
logger.warning ('WARNING: alignments cmp.h5 file should now be specified with --aln keyword')
opt.aln = args.pop() # put it where it belongs
return opt, args
def getGeneFromAnnotation(opt, tranList, exonList):
# Add to lists of transcripts and exons: annotations for gene of interest.
if opt.gtf is None:
return tranList, exonList
if opt.annotations:
annotList = opt.annotations
else:
if opt.format == 'pickle':
annotList = anno.AnnotationList.fromPickle(opt.gtf)
elif opt.format == 'alt':
annotList = anno.AnnotationList(opt.gtf, altFormat=True)
else: # standard format
annotList = anno.AnnotationList(opt.gtf)
allGenes = annotList.getGeneDict()
allGenes.update({k.upper(): v for k, v in allGenes.iteritems()})
if opt.gene not in allGenes:
raise RuntimeError('gene %s is not in the annotation file' % opt.gene)
geneList = allGenes[opt.gene] # a list of Annotation objects
if len(geneList) > 1:
logger.warning('gene %s appears %d times in annotations, first occurrence plotted'
% (opt.gene, len(geneList)))
myGene = geneList[0]
for tran in myGene.getChildren(): # tran is an Annotation object
myTran = Transcript(tran.name, start=tran.start, end=tran.end,
annot=True, ID=tran.ID, source=(0, opt.gtf))
if hasattr(tran, 'startcodon'):
myTran.startcodon = tran.startcodon
if hasattr(tran, 'stopcodon'):
myTran.stopcodon = tran.stopcodon
for exon in tran.getChildren(): # exon is an Annotation object
myExon = Exon(myTran, exon.name, exon.start,
exon.end, exon.strand) # no Q score
if hasattr(exon, 'polyAs'):
myExon.polyAs = exon.polyAs
exonList.append(myExon)
myTran.exons.append(myExon)
tranList.append(myTran)
return tranList, exonList
def main ():
logger.debug("%s starting" % sys.argv[0])
opt, args = getParms()
basFilename = args[0]
logger.debug("bas file: %s" % basFilename)
bf = H5BasFile.BasFile (basFilename, CCSDir=opt.ccs)
if not opt.nocons:
if not bf.hasConsensus():
logger.warning('no ccs data found: turning on --nocons')
opt.nocons = True
cmp = None # no cmp file?
if opt.aln is not None: # was a subread cmp.h5 file specified?
cmpFilename = opt.aln
logger.debug("cmp file: %s" % cmpFilename)
cf = H5CmpFile.CmpFile (fileName=cmpFilename)
cmp = H5CmpFile.CmpMovie (cmpObject=cf,
movieName=bf.movieName(),
maxHole=bf.maxZMW())
cmpCCS = None
if opt.alnccs is not None: # was a CCS cmp.h5 file specified?
cmpCCSFilename = opt.alnccs
logger.debug("CCS cmp file: %s" % cmpCCSFilename)
cfCCS = H5CmpFile.CmpFile (fileName=cmpCCSFilename)
cmpCCS = H5CmpFile.CmpMovie (cmpObject=cfCCS,
movieName=bf.movieName(),
maxHole=bf.maxZMW())
aln = SWAligner.Aligner() # we'll use this in the loop below for finding adapters
aln.setRead (H5BasFile.ADAPTER) # adapter sequence is query
minAdapterScore = opt.adapter * aln.getPenalties()[0] / 2
print " ZMW b/s stat prod tp start end+1 len aln chr st",
print " from to off astart aend+1 mm ins del Q"
print
for hole in bf.holeNumbers(): # main loop!
numBases = bf.readLen(hole)
zStat = bf.holeStatusStr(hole) # this is a string, not a number
zProd = bf.productivity(hole)
numGoodInserts = 0
HQStart, HQEnd, HQScore = bf.HQregion(hole)[2:5]
for region in bf.holeRegions(hole):
regionHole, regionType, start, end, score = region
inHQ = end > HQStart and start < HQEnd # does region overlap HQ?
regionDuration = float(bf.elapsedFrames(hole, start, end)) / H5BasFile.frameRate
regionBps = (end-start) / regionDuration if regionDuration > 0 else 0
if regionType == 0: # an adapter region?
if not opt.noadapt: # if we are printing adapter lines
print "%6d %6.3f %-5s %d" % (hole, regionBps, zStat, zProd), # these appear in every line
flag = 'A ' if inHQ else 'a '
print "%-2s %5d %5d" % (flag, start, end)
elif regionType == 2: # a HQ region?
print "%6d %6.3f %-5s %d" % (hole, regionBps, zStat, zProd), # these appear in every line
if zProd != 1 or not bf.isSequencingZMW(hole) or (HQEnd-HQStart) < opt.length:
flag = 'h '
else:
flag = 'H+' if score >= opt.score else 'H '
print "%-2s %5d %5d" % (flag, start, end),
readDuration = float(bf.elapsedFrames(hole)) / H5BasFile.frameRate
readBps = numBases/readDuration if readDuration > 0 else 0
print " score: %3d HQ: %5d read: %5d dur: %8.3f b/sec: %6.3f" \
% (score, HQEnd-HQStart, numBases, readDuration, readBps)
elif regionType == 1: # a subread?
print "%6d %6.3f %-5s %d" % (hole, regionBps, zStat, zProd), # these appear in every line
insSize = end - start
align = None
if cmp is not None: # if a cmp.h5 was supplied
align = cmp.getAlignmentByPosition (hole, start, end) # alignment record for this region
if align is not None: # if the region aligned
numGoodInserts += 1
flag = 'I+'
print "%-2s %5d %5d %5d" % (flag, start, end, insSize),
rStart, rEnd = align['rStart'], align['rEnd'] # fetch once, used many times
alnLen = rEnd-rStart
nMM, nIns, nDel = align['nMM'], align['nIns'], align['nDel']
print "%5d %2d %1s %9d %9d %4d %6d %6d %3d %4d %3d %4.1f" % \
(alnLen, # length of aligned portion of read
align['contig'], # chr/contig id (see H5CmpFile)
'-' if align['RCRefStrand'] else '+', # strand
align['tStart'], align['tEnd'], # reference offset of start/end of alignment
rStart-start, # offset of alignment start into insert
rStart, rEnd,
nMM, nIns, nDel, # # of mismatches, insertions, deletions
getQ (align)), # read quality Q score for insert
elif insSize > opt.adapter * 2: # if it's a non-descript, non-aligned region
# TODO: Make the '2' a parameter
numGoodInserts += 1
flag = 'I ' if inHQ else 'i '
print "%-2s %5d %5d %5d" % (flag, start, end, insSize),
elif insSize < opt.adapter: # if it's too short to be an adapter
flag = 'Is' if inHQ else 'is'
print "%-2s %5d %5d %5d" % (flag, start, end, insSize),
else: # see if it's really an adapter that wasn't called
sequence = bf.getSequence(hole, start, end)
aln.setRef (sequence)
alnScore = aln.fillMatrix() # align it to adapter
flag = 'ia' if alnScore >= minAdapterScore else 'is'
print "%-2s %5d %5d %5d %2d" % (flag, start, end, insSize, alnScore),
if alnScore >= minAdapterScore:
peaks = aln.peakPosits()
print " %2d" % len(peaks),
refString, readString = aln.alignmentStrings()
print ' ', refString # EOL here
print " i2 ", # new line
print readString,
print
else:
raise ValueError ("unrecognised region type %d in ZMW %d" % (regionType, hole))
if not opt.nocons: # note that opt.nocons gets turned on if no CCS data is found
if zProd == 1 and bf.isSequencingZMW(hole):
printCCSDataForHole (bf, hole, numGoodInserts, cmpCCS) # process consensus read passes
logger.debug("complete")
def main ():
logger.debug("%s starting" % sys.argv[0])
opt, args = getParms()
basFilename = args[0]
logger.debug("bas file: %s" % basFilename)
bf = H5BasFile.BasFile (basFilename, CCSDir=opt.ccs)
if bf.hasConsensus(): # don't go looking for CCS data if it's not there
nocons = False
else:
logger.warning('no ccs data found: point to it with --ccs if desired')
nocons = True
cmp = None # no cmp file?
if opt.aln is not None: # was a subread cmp.h5 file specified?
cmpFilename = opt.aln
logger.debug("cmp file: %s" % cmpFilename)
cf = H5CmpFile.CmpFile (fileName=cmpFilename)
cmp = H5CmpFile.CmpMovie (cmpObject=cf,
movieName=bf.movieName(),
maxHole=bf.maxZMW())
totalC = Counter('Total')
seqC = Counter('--Sequencing')
prod0C = Counter('----Productivity-0')
prod1C = Counter('----Productivity-1')
HQLenC = Counter('------HQ Len >= %s' % opt.length)
HQScoreC = Counter('--------HQ Score >= %s' % opt.score)
adaptC = Counter('----------Avg Insert >= %s' % opt.insert)
HQBasesC = Counter('----------HQ Bases')
alignC = Counter('------------Aligned')
consC = Counter('------------Consensus Reads')
prod2C = Counter('----Productivity-2')
longest = 0
longestZMW = None
for hole in bf.holeNumbers():
numBases = bf.readLen(hole)
zProd = bf.productivity(hole)
if numBases > longest:
longest = numBases
longestZMW = hole
HQStart, HQEnd, HQScore = bf.HQregion(hole)[2:5]
HQLen = HQEnd - HQStart
numSubreads = 0
numHQSubreads = 0
maxSubreadLen = 0
cumSubreadLen = 0
alignedSubreads = 0
alignedTotBases = 0 # total aligned bases in all inserts
alignedMaxBases = 0 # longest alignment in single insert
for region in bf.holeRegions(hole):
regionHole, regionType, start, end, score = region
inHQ = end > HQStart and start < HQEnd # does region overlap HQ?
if regionType == 1: # if insert
numSubreads += 1
maxSubreadLen = max (end-start, maxSubreadLen)
cumSubreadLen += max (end-start, 0) # clip negative lengths to zero
if inHQ:
numHQSubreads += 1
if cmp is not None:
align = cmp.getAlignmentByPosition (hole, start, end) # alignment record for this region
if align is not None: # if the region aligned
alignedSubreads += 1
alignedBases = align['rEnd'] - align ['rStart']
alignedTotBases += alignedBases
alignedMaxBases = max (alignedBases, alignedMaxBases)
# What follows is a series of increasingly restrictive
# criteria for a useful subread. Keep track of the number of
# ZMWs, subreads, and bases which pass the successive tests,
# and the length and ZMW provenance of the longest accepted
# subread.
totalC.incr (1, numSubreads, numBases)
totalC.longest (hole, maxSubreadLen)
if bf.isSequencingZMW(hole): # sequencing ZMW?
seqC.incr (1, numSubreads, numBases)
seqC.longest (hole, maxSubreadLen)
if zProd == 0:
prod0C.incr (1, numSubreads, numBases)
prod0C.longest (hole, maxSubreadLen)
elif zProd == 2:
prod2C.incr (1, numSubreads, numBases)
prod2C.longest (hole, maxSubreadLen)
elif zProd == 1: # productivity 1 gets broken down further
prod1C.incr (1, numSubreads, numBases)
prod1C.longest (hole, maxSubreadLen)
if HQLen >= opt.length:
HQLenC.incr (1, numSubreads, numBases)
HQLenC.longest (hole, maxSubreadLen)
if HQScore >= opt.score:
HQScoreC.incr (1, numSubreads, numBases)
HQScoreC.longest (hole, maxSubreadLen)
# A very short average insert size probably indicates an adapter dimer.
if cumSubreadLen >= numSubreads * opt.insert:
adaptC.incr (1, numSubreads, numBases)
adaptC.longest (hole, maxSubreadLen)
HQBasesC.incr (1, numHQSubreads, HQLen) #
HQBasesC.longest (hole, HQLen)
if alignedSubreads > 0:
alignC.incr (1, alignedSubreads, alignedTotBases) # total aligned bases
alignC.longest (hole, alignedMaxBases) # longest single alignment
if not nocons:
consLen = bf.consReadLen(hole)
if consLen > 0:
consC.incr (1, bf.numConsensusPasses(hole), consLen)
consC.longest (hole, consLen)
print
print "file: ", basFilename
print
print "longest read was ZMW %d at %d bases" % (longestZMW, longest)
print
print "statistics for subreads:"
print
Counter.title();
if cmp is not None: # if we processed a .cmp.h5 file
for cntr in (totalC, seqC, prod0C, prod2C, prod1C, HQLenC, HQScoreC, adaptC, HQBasesC, consC, alignC):
cntr.longPrint()
else:
for cntr in (totalC, seqC, prod0C, prod2C, prod1C, HQLenC, HQScoreC, adaptC, HQBasesC, consC):
cntr.longPrint()
print
logger.debug("complete")
def main():
logger.debug("%s starting" % sys.argv[0])
opt, args = getParms()
basFilename = args[0]
logger.debug("bas file: %s" % basFilename)
bf = H5BasFile.BasFile(basFilename, CCSDir=opt.ccs)
if not opt.nocons:
if not bf.hasConsensus():
logger.warning('no ccs data found: turning on --nocons')
opt.nocons = True
cmp = None # no cmp file?
if opt.aln is not None: # was a subread cmp.h5 file specified?
cmpFilename = opt.aln
logger.debug("cmp file: %s" % cmpFilename)
cf = H5CmpFile.CmpFile(fileName=cmpFilename)
cmp = H5CmpFile.CmpMovie(cmpObject=cf,
movieName=bf.movieName(),
maxHole=bf.maxZMW())
cmpCCS = None
if opt.alnccs is not None: # was a CCS cmp.h5 file specified?
cmpCCSFilename = opt.alnccs
logger.debug("CCS cmp file: %s" % cmpCCSFilename)
cfCCS = H5CmpFile.CmpFile(fileName=cmpCCSFilename)
cmpCCS = H5CmpFile.CmpMovie(cmpObject=cfCCS,
movieName=bf.movieName(),
maxHole=bf.maxZMW())
aln = SWAligner.Aligner(
) # we'll use this in the loop below for finding adapters
aln.setRead(H5BasFile.ADAPTER) # adapter sequence is query
minAdapterScore = opt.adapter * aln.getPenalties()[0] / 2
print " ZMW b/s stat prod tp start end+1 len aln chr st",
print " from to off astart aend+1 mm ins del Q"
print
for hole in bf.holeNumbers(): # main loop!
numBases = bf.readLen(hole)
zStat = bf.holeStatusStr(hole) # this is a string, not a number
zProd = bf.productivity(hole)
numGoodInserts = 0
HQStart, HQEnd, HQScore = bf.HQregion(hole)[2:5]
for region in bf.holeRegions(hole):
regionHole, regionType, start, end, score = region
inHQ = end > HQStart and start < HQEnd # does region overlap HQ?
regionDuration = float(bf.elapsedFrames(hole, start,
end)) / H5BasFile.frameRate
regionBps = (end -
start) / regionDuration if regionDuration > 0 else 0
if regionType == 0: # an adapter region?
if not opt.noadapt: # if we are printing adapter lines
print "%6d %6.3f %-5s %d" % (
hole, regionBps, zStat,
zProd), # these appear in every line
flag = 'A ' if inHQ else 'a '
print "%-2s %5d %5d" % (flag, start, end)
elif regionType == 2: # a HQ region?
print "%6d %6.3f %-5s %d" % (
hole, regionBps, zStat,
zProd), # these appear in every line
if zProd != 1 or not bf.isSequencingZMW(hole) or (
HQEnd - HQStart) < opt.length:
flag = 'h '
else:
flag = 'H+' if score >= opt.score else 'H '
print "%-2s %5d %5d" % (flag, start, end),
readDuration = float(
bf.elapsedFrames(hole)) / H5BasFile.frameRate
readBps = numBases / readDuration if readDuration > 0 else 0
print " score: %3d HQ: %5d read: %5d dur: %8.3f b/sec: %6.3f" \
% (score, HQEnd-HQStart, numBases, readDuration, readBps)
elif regionType == 1: # a subread?
print "%6d %6.3f %-5s %d" % (
hole, regionBps, zStat,
zProd), # these appear in every line
insSize = end - start
align = None
if cmp is not None: # if a cmp.h5 was supplied
align = cmp.getAlignmentByPosition(
hole, start, end) # alignment record for this region
if align is not None: # if the region aligned
numGoodInserts += 1
flag = 'I+'
print "%-2s %5d %5d %5d" % (flag, start, end, insSize),
rStart, rEnd = align['rStart'], align[
'rEnd'] # fetch once, used many times
alnLen = rEnd - rStart
nMM, nIns, nDel = align['nMM'], align['nIns'], align[
'nDel']
print "%5d %2d %1s %9d %9d %4d %6d %6d %3d %4d %3d %4.1f" % \
(alnLen, # length of aligned portion of read
align['contig'], # chr/contig id (see H5CmpFile)
'-' if align['RCRefStrand'] else '+', # strand
align['tStart'], align['tEnd'], # reference offset of start/end of alignment
rStart-start, # offset of alignment start into insert
rStart, rEnd,
nMM, nIns, nDel, # # of mismatches, insertions, deletions
getQ (align)), # read quality Q score for insert
elif insSize > opt.adapter * 2: # if it's a non-descript, non-aligned region
# TODO: Make the '2' a parameter
numGoodInserts += 1
flag = 'I ' if inHQ else 'i '
print "%-2s %5d %5d %5d" % (flag, start, end, insSize),
elif insSize < opt.adapter: # if it's too short to be an adapter
flag = 'Is' if inHQ else 'is'
print "%-2s %5d %5d %5d" % (flag, start, end, insSize),
else: # see if it's really an adapter that wasn't called
sequence = bf.getSequence(hole, start, end)
aln.setRef(sequence)
alnScore = aln.fillMatrix() # align it to adapter
flag = 'ia' if alnScore >= minAdapterScore else 'is'
print "%-2s %5d %5d %5d %2d" % (flag, start, end,
insSize, alnScore),
if alnScore >= minAdapterScore:
peaks = aln.peakPosits()
print " %2d" % len(peaks),
refString, readString = aln.alignmentStrings()
print ' ', refString # EOL here
print " i2 ", # new line
print readString,
print
else:
raise ValueError("unrecognised region type %d in ZMW %d" %
(regionType, hole))
if not opt.nocons: # note that opt.nocons gets turned on if no CCS data is found
if zProd == 1 and bf.isSequencingZMW(hole):
printCCSDataForHole(bf, hole, numGoodInserts,
cmpCCS) # process consensus read passes
logger.debug("complete")
