def removeOutliers(self, binFile, outlierFile, outputFile):
"""Remove sequences specified as outliers in the provided file."""
binSeqs = readFasta(binFile)
binIdToModify = binIdFromFilename(binFile)
# get files to remove
checkFileExists(outlierFile)
seqsToRemove = []
bHeader = True
for line in open(outlierFile):
if bHeader:
bHeader = False
continue
lineSplit = line.split('\t')
binId = lineSplit[0]
if binId == binIdToModify:
seqId = lineSplit[1]
seqsToRemove.append(seqId)
# remove sequences from bin
if len(seqsToRemove) > 0:
self.__removeSeqs(binSeqs, seqsToRemove)
# save modified bin
writeFasta(binSeqs, outputFile)
def run(self, coverageFile, outFile, bTabTable):
checkFileExists(coverageFile)
# get number of reads mapped to each bin
self.logger.info('Determining number of reads mapped to each bin.')
readsMappedToBin = {}
binSize = {}
totalMappedReads = {}
bHeader = True
for line in open(coverageFile):
if bHeader:
bHeader = False
continue
lineSplit = line.split('\t')
# seqId = lineSplit[0]
binId = lineSplit[1]
seqLen = int(lineSplit[2])
binSize[binId] = binSize.get(binId, 0) + seqLen
if binId not in readsMappedToBin:
readsMappedToBin[binId] = {}
for i in xrange(3, len(lineSplit), 3):
bamId = lineSplit[i]
mappedReads = int(lineSplit[i + 2])
totalMappedReads[bamId] = totalMappedReads.get(bamId,
0) + mappedReads
readsMappedToBin[binId][bamId] = readsMappedToBin[binId].get(
bamId, 0) + mappedReads
# calculate percentage of mapped reads to binned populations
perMappedReads = {}
normBinCoverage = {}
sumNormBinCoverage = {}
for binId, bamIds in readsMappedToBin.iteritems():
perMappedReads[binId] = {}
normBinCoverage[binId] = {}
for bamId in bamIds:
perMR = float(
readsMappedToBin[binId][bamId]) / totalMappedReads[bamId]
perMappedReads[binId][bamId] = perMR
if binId == DefaultValues.UNBINNED:
continue
normCoverage = perMR / binSize[binId]
normBinCoverage[binId][bamId] = normCoverage
sumNormBinCoverage[bamId] = sumNormBinCoverage.get(
bamId, 0) + normCoverage
for binId, bamIds in normBinCoverage.iteritems():
for bamId in bamIds:
if sumNormBinCoverage[bamId] != 0:
normBinCoverage[binId][bamId] /= sumNormBinCoverage[bamId]
else:
normBinCoverage[binId][bamId] = 0
# write community profile
oldStdOut = reassignStdOut(outFile)
sortedBinIds = sorted(readsMappedToBin.keys())
sortedBamIds = sorted(readsMappedToBin[sortedBinIds[0]].keys())
header = ['Bin Id', 'Bin size (Mbp)']
for bamId in sortedBamIds:
header += [bamId + ': mapped reads']
header += [bamId + ': % mapped reads']
header += [bamId + ': % binned populations']
header += [bamId + ': % community']
if bTabTable:
print('\t'.join(header))
else:
pTable = prettytable.PrettyTable(header)
pTable.float_format = '.2'
pTable.align = 'c'
pTable.align[header[0]] = 'l'
pTable.hrules = prettytable.FRAME
pTable.vrules = prettytable.NONE
for binId in sortedBinIds:
row = [binId]
row += [float(binSize[binId]) / 1e6]
for bamId in sortedBamIds:
row += [readsMappedToBin[binId][bamId]]
row += [perMappedReads[binId][bamId] * 100.0]
if DefaultValues.UNBINNED in perMappedReads:
unbinnedPercentage = perMappedReads[
DefaultValues.UNBINNED][bamId]
else:
unbinnedPercentage = 0
if binId == DefaultValues.UNBINNED:
row += ['NA']
row += [unbinnedPercentage * 100.0]
else:
row += [normBinCoverage[binId][bamId] * 100.0]
row += [
normBinCoverage[binId][bamId] * 100.0 *
(1.0 - unbinnedPercentage)
]
if bTabTable:
print('\t'.join(map(str, row)))
else:
pTable.add_row(row)
if not bTabTable:
print(pTable.get_string())
restoreStdOut(outFile, oldStdOut)
def run(self, coverageFile, outFile, bTabTable):
checkFileExists(coverageFile)
# get number of reads mapped to each bin
self.logger.info(' Determining number of reads mapped to each bin.')
self.logger.info('')
readsMappedToBin = {}
binSize = {}
totalMappedReads = {}
bHeader = True
for line in open(coverageFile):
if bHeader:
bHeader = False
continue
lineSplit = line.split('\t')
# seqId = lineSplit[0]
binId = lineSplit[1]
seqLen = int(lineSplit[2])
binSize[binId] = binSize.get(binId, 0) + seqLen
if binId not in readsMappedToBin:
readsMappedToBin[binId] = {}
for i in xrange(3, len(lineSplit), 3):
bamId = lineSplit[i]
mappedReads = int(lineSplit[i + 2])
totalMappedReads[bamId] = totalMappedReads.get(bamId, 0) + mappedReads
readsMappedToBin[binId][bamId] = readsMappedToBin[binId].get(bamId, 0) + mappedReads
# calculate percentage of mapped reads to binned populations
perMappedReads = {}
normBinCoverage = {}
sumNormBinCoverage = {}
for binId, bamIds in readsMappedToBin.iteritems():
perMappedReads[binId] = {}
normBinCoverage[binId] = {}
for bamId in bamIds:
perMR = float(readsMappedToBin[binId][bamId]) / totalMappedReads[bamId]
perMappedReads[binId][bamId] = perMR
if binId == DefaultValues.UNBINNED:
continue
normCoverage = perMR / binSize[binId]
normBinCoverage[binId][bamId] = normCoverage
sumNormBinCoverage[bamId] = sumNormBinCoverage.get(bamId, 0) + normCoverage
for binId, bamIds in normBinCoverage.iteritems():
for bamId in bamIds:
normBinCoverage[binId][bamId] /= sumNormBinCoverage[bamId]
# write community profile
oldStdOut = reassignStdOut(outFile)
sortedBinIds = sorted(readsMappedToBin.keys())
sortedBamIds = sorted(readsMappedToBin[sortedBinIds[0]].keys())
header = ['Bin Id', 'Bin size (Mbp)']
for bamId in sortedBamIds:
header += [bamId + ': mapped reads']
header += [bamId + ': % mapped reads']
header += [bamId + ': % binned populations']
header += [bamId + ': % community']
if bTabTable:
print('\t'.join(header))
else:
pTable = prettytable.PrettyTable(header)
pTable.float_format = '.2'
pTable.align = 'c'
pTable.align[header[0]] = 'l'
pTable.hrules = prettytable.FRAME
pTable.vrules = prettytable.NONE
for binId in sortedBinIds:
row = [binId]
row += [float(binSize[binId]) / 1e6]
for bamId in sortedBamIds:
row += [readsMappedToBin[binId][bamId]]
row += [perMappedReads[binId][bamId] * 100.0]
if DefaultValues.UNBINNED in perMappedReads:
unbinnedPercentage = perMappedReads[DefaultValues.UNBINNED][bamId]
else:
unbinnedPercentage = 0
if binId == DefaultValues.UNBINNED:
row += ['NA']
row += [unbinnedPercentage * 100.0]
else:
row += [normBinCoverage[binId][bamId] * 100.0]
row += [normBinCoverage[binId][bamId] * 100.0 * (1.0 - unbinnedPercentage)]
if bTabTable:
print('\t'.join(map(str, row)))
else:
pTable.add_row(row)
if not bTabTable:
print(pTable.get_string())
restoreStdOut(outFile, oldStdOut)
