/usr/lib/python2.7/dist-packages/pbbarcode/BarcodeLabeler.py is in pbbarcode 0.8.0-1.
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# Copyright (c) 2011,2012, 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.
#
# 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.
#################################################################################$$
import logging
from pbcore.io import BasH5Reader, BaxH5Reader
from pbcore.io.FastaIO import *
import pbbarcode.SWaligner as Aligner
import numpy as n
from pbcore.io.BarcodeH5Reader import LabeledZmw, \
BARCODE_DELIMITER
__RC_MAP__ = dict(zip('ACGTacgt-N','TGCAtgca-N'))
class BarcodeScorer(object):
def __init__(self, basH5, barcodeFasta,
adapterSidePad = 0, insertSidePad = 4,
scoreMode = 'symmetric', maxHits = 10,
scoreFirst = False, startTimeCutoff = 1):
"""A BarcodeScorer object scores ZMWs and produces summaries
of the scores. Various parameters control the behavior of the
object, specifically the padding allows the user to add a
little extra on each side of the adapter find for safety. The
most relevant parameter is the scoreMode which dictates how
the barcodes are scored, either paired or symmetric."""
self.basH5 = basH5
self.barcodeFasta = list(barcodeFasta)
self.aligner = Aligner.SWaligner()
self.barcodeLength = n.unique(map(lambda x : len(x.sequence),
self.barcodeFasta))
if len(self.barcodeLength) > 1:
raise Exception("Currently, all barcodes must be the same length.")
else:
self.barcodeLength = int(self.barcodeLength)
self.barcodeSeqs = [(barcode.sequence.upper(),
self._rc(barcode.sequence.upper()))
for barcode in self.barcodeFasta]
self.adapterSidePad = adapterSidePad
self.insertSidePad = insertSidePad
self.maxHits = maxHits
if scoreMode not in ['symmetric', 'paired']:
raise Exception("scoreMode must either be symmetric or paired")
self._scoreMode = scoreMode
self.scoreFirst = scoreFirst
self.startTimeCutoff = startTimeCutoff
self.forwardScorer = self.aligner.makeScorer([x[0] for x in self.barcodeSeqs])
self.reverseScorer = self.aligner.makeScorer([x[1] for x in self.barcodeSeqs])
logging.debug(("Constructed BarcodeScorer with scoreMode: %s," + \
"adapterSidePad: %d, insertSidePad: %d, and scoreFirst: %r") \
% (scoreMode, adapterSidePad, insertSidePad, scoreFirst))
@property
def movieName(self):
return self.basH5.movieName
def makeBCLabel(self, s1, s2):
return BARCODE_DELIMITER.join((s1, s2))
@property
def barcodeLabels(self):
"""The barcode labels are function of the barcodeNames and the
scoreMode, they represent the user-visible names."""
if self.scoreMode == 'paired':
return n.array([self.makeBCLabel(self.barcodeFasta[i].name,
self.barcodeFasta[i+1].name) for i
in xrange(0, len(self.barcodeSeqs), 2)])
else:
return n.array([self.makeBCLabel(x.name, x.name) for x in self.barcodeFasta])
@property
def barcodeNames(self):
"""The barcode names are the FASTA names"""
return n.array([x.name for x in self.barcodeFasta])
@property
def scoreMode(self):
return self._scoreMode
def _rc(self, s):
return "".join([__RC_MAP__[c] for c in s[::-1]])
def _flankingSeqs(self, zmw):
def fromRange(rStart, rEnd):
try:
qSeqLeft = zmw.read(rStart - (self.barcodeLength + self.insertSidePad),
rStart + self.adapterSidePad).basecalls()
except IndexError:
qSeqLeft = None
try:
qSeqRight = zmw.read(rEnd - self.adapterSidePad,
rEnd + self.barcodeLength +
self.insertSidePad).basecalls()
except IndexError:
qSeqRight = None
return (qSeqLeft, qSeqRight)
adapterRegions = zmw.adapterRegions
if len(adapterRegions) > self.maxHits:
adapterRegions = adapterRegions[0:self.maxHits]
seqs = [fromRange(start, end) for (start, end) in adapterRegions]
# We only score the first barcode if we don't find any adapters
# *and* the start time is less than the threshold.
scoredFirst = False
if self.scoreFirst and not len(seqs):
s = zmw.zmwMetric('HQRegionStartTime')
e = zmw.zmwMetric('HQRegionEndTime')
# s<e => has HQ.
if s < e and s <= self.startTimeCutoff:
l = self.barcodeLength + self.insertSidePad
l = l if zmw.hqRegion[1] > l else zmw.hqRegion[1]
try:
bc = zmw.read(0, l).basecalls()
if len(bc) >= self.barcodeLength:
seqs.insert(0, (bc, None))
scoredFirst = True
except IndexError:
pass
return (seqs, scoredFirst)
def labelZmws(self, holeNumbers):
"""Return a list of LabeledZmws for input holeNumbers"""
def scoreZmw(zmw):
adapters, scoredFirst = self._flankingSeqs(zmw)
adapterScores = [[]]*len(adapters)
barcodeScores = n.zeros(len(self.barcodeSeqs))
for i,adapter in enumerate(adapters):
fscores = self.forwardScorer(adapter[0])
rscores = self.reverseScorer(adapter[0])
ffscores = self.forwardScorer(adapter[1])
rrscores = self.reverseScorer(adapter[1])
scored = 2.0 if adapter[0] and adapter[1] else \
1.0 if adapter[0] or adapter[1] else 0
# An adapter score is the average barcode score for
# each barcode -- that way, you can compare across
# adapters even if the different adapters have
# different numbers of flanking sequence.
if scored == 0:
adapterScores[i] = barcodeScores
else:
adapterScores[i] = n.maximum((fscores + rrscores)/scored,
(rscores + ffscores)/scored)
barcodeScores = reduce(lambda x, y: x + y, adapterScores) if adapterScores \
else n.zeros(len(self.barcodeSeqs))
return (zmw.holeNumber, len(adapters), barcodeScores, adapterScores,
scoredFirst)
# o here is the record immediately above.
def chooseSymmetric(o):
p = n.argsort(-o[2])
return LabeledZmw(o[0], o[1], p[0], o[2][p[0]], p[1], o[2][p[1]], o[3])
def choosePaired(o):
if o[1] == 1:
s = n.array([max(o[2][i], o[2][i + 1]) for i in \
xrange(0, len(self.barcodeSeqs), 2)])
p = n.argsort(-s)
s = s[p]
else:
# score the pairs by scoring the two alternate
# ways they could have been put on the molecule. A
# missed adapter will confuse this computation.
scores = o[3]
results = n.zeros(len(self.barcodeSeqs)/2)
for i in xrange(0, len(self.barcodeSeqs), 2):
pths = [0,0]
for j in xrange(0, len(scores)):
pths[j % 2] += scores[j][i]
pths[1 - j % 2] += scores[j][i + 1]
results[i/2] = max(pths)
p = n.argsort(-results)
s = results[p]
return LabeledZmw(o[0], o[1], p[0], s[0], p[1], s[1], o[3])
if self.scoreMode == 'symmetric':
choose = chooseSymmetric
elif self.scoreMode == 'paired':
choose = choosePaired
else:
raise Exception("Unsupported scoring mode in BarcodeLabeler.py")
scored = [scoreZmw(self.basH5[zmw]) for zmw in holeNumbers]
return [choose(scoreTup) for scoreTup in scored if scoreTup[1]]
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