def runAll(args):
print('\n\n\nYou have requested to count unique sam files')
print('\tWARNING:')
print('\t\tIF USING ANY REFERENCES OTHER THAN THOSE I PROVIDE I CANNOT GUARANTEE RESULT ACCURACY')
print('\n')
#set up environment#
args.SamDirectory = common.fixDirName(args.SamDirectory)
countDir = os.path.dirname(args.SamDirectory[:-1]) + '/BinCounts/'
if args.output:
countDir = common.fixDirName(args.output)
statsDir = os.path.dirname(args.SamDirectory[:-1]) + '/PipelineStats/'
if args.statdir:
statsDir = common.fixDirName(args.statdir)
for i in [countDir, statsDir]:
common.makeDir(i)
samFiles = common.getSampleList(args.SamDirectory, args.samples, 'sam')
#run multiprocessing of all bin counting commands#
argList = [(x, countDir, statsDir, args.species) for x in samFiles]
common.daemon(countfile.runOne, argList, 'count sam files')
print('\nBin counts complete\n\n\n')
def runAll(args):
print('\n\n\nYou have requested preprocess (trim) fastq files')
print('\tWARNING:')
print('\t\tIF USING ANY LENGTH OTHER THAN 36 BP, REFERENCE FILES ARE NOT SUPPORTED FOR DOWNSTREAM PROCESSING')
print('\n')
#make sure environment is properly prepared#
args.FastqDirectory = common.fixDirName(args.FastqDirectory)
if not args.remove:
common.makeDir(args.FastqDirectory + '/FullLength/')
#get list of fastq files to process (depending on args.samples)
fastqFiles = common.getSampleList(args.FastqDirectory, args.samples, 'fastq')
#use the daemon to and preprocessing code to trim all fastq files with parallel processing
if args.remove:
argList = [(x, args.trim5, args.length, remove=True,) for x in fastqFiles]
else:
argList = [(x, args.trim5, args.length,) for x in fastqFiles]
common.daemon(trimfile.preprocessOne, argList, 'trim sequencing reads to desired length', cpuPerProcess=1)
print('\nPre-processing complete\n\n\n')
def runAll(args):
print('\n\n\nYou have requested to map fastq files')
print('\tWARNING:')
print('\t\tIF USING ANY REFERENCES OTHER THAN THOSE I PROVIDE I CANNOT GUARANTEE RESULT ACCURACY')
print('\n')
#set up environment#
args.FastqDirectory = common.fixDirName(args.FastqDirectory)
samDir = os.path.dirname(args.FastqDirectory[:-1]) + '/Sam/'
if args.output:
samDir = common.fixDirName(args.output)
statsDir = os.path.dirname(args.FastqDirectory[:-1]) + '/PipelineStats/'
if args.statdir:
statsDir = common.fixDirName(args.statdir)
tempDir = args.FastqDirectory + 'Temp/'
for i in [samDir, tempDir, statsDir]:
common.makeDir(i)
fastqFiles = common.getSampleList(args.FastqDirectory, args.samples, 'fastq')
#run multiprocessing of all mapping commands#
argList = [(x, args.species, args.trim, statsDir, tempDir, samDir) for x in fastqFiles]
common.daemon(mapfile.runOne, argList, 'map fastq files', cpuPerProcess=8)
#remove all temporary files#
shutil.rmtree(tempDir[:-1])
print('\nMapping complete\n\n\n')
def runAll(args):
print('\n\n\nYou have requested to map fastq files')
print('\tWARNING:')
print('\t\tPLEASE MAKE SURE YOU ARE USING')
print('\t\t\tBowtie v1 and Samtools v0.1.19')
print('\t\t\tBowtie v1 mapping indexes for either mm10 or hg38')
print('\n')
#set up environment#
args.FastqDirectory = common.fixDirName(args.FastqDirectory)
samDir = os.path.dirname(args.FastqDirectory[:-1]) + '/Sam/'
if args.output:
samDir = common.fixDirName(args.output)
statsDir = os.path.dirname(args.FastqDirectory[:-1]) + '/PipelineStats/'
if args.statdir:
statsDir = common.fixDirName(args.statdir)
tempDir = args.FastqDirectory + 'Temp/'
for i in [samDir, tempDir, statsDir]:
common.makeDir(i)
fastqFiles = common.getSampleList(args.FastqDirectory, args.samples,
'fastq')
#run multiprocessing of all mapping commands#
argList = [(x, args.MapIndex, args.trim, statsDir, tempDir, samDir,
args.bowtie, args.samtools) for x in fastqFiles]
common.daemon(mapfile.runOne, argList, 'map fastq files', cpuPerProcess=8)
#remove all temporary files#
shutil.rmtree(tempDir[:-1])
print('\nMapping complete\n\n\n')
def runAll(args):
print('\n\n\nYou have requested to normalize and segment bincounts files')
print('\tWARNING:')
print(
'\t\tIF USING ANY REFERENCES OTHER THAN THOSE I PROVIDE I CANNOT GUARANTEE RESULT ACCURACY'
)
print('\n')
#Set up environment#
args.AnalysisDirectory = common.fixDirName(args.AnalysisDirectory)
CountDir = args.AnalysisDirectory + 'BinCounts/' #args.CountDirectory = common.fixDirName(args.CountDirectory)
if args.bincountdir:
CountDir = common.fixDirName(args.bincountdir)
lowessDir = args.AnalysisDirectory + 'LowessBinCounts/' #os.path.dirname(args.CountDirectory[:-1]) + '/LowessBinCounts/'
segmentDir = args.AnalysisDirectory + 'Segments/' #os.path.dirname(args.CountDirectory[:-1]) + '/Segments/'
tempDir = args.AnalysisDirectory + 'Temp/' #os.path.dirname(args.CountDirectory[:-1]) + '/Temp/'
common.makeDir(lowessDir)
if not args.normalizeonly:
common.makeDir(segmentDir)
common.makeDir(tempDir)
sampleFiles = common.getSampleList(CountDir, args.samples, 'bincounts')
info = common.importInfoFile(args.infofile, args.columns, 'normalize')
if args.infofile:
refArray = info
else:
thisDtype = info
refArray = np.array([(
os.path.basename(x)[:-14],
'unk',
1,
) for x in sampleFiles],
dtype=thisDtype)
sampleDict = {
x: [y for y in sampleFiles if x == os.path.basename(y)[:len(x)]][0]
for x in refArray['name']
}
#Run normalization for all samples#
methodDict = {x: [
False,
]
for x in np.unique(refArray['method'])}
methodDict['NA'] = [False]
sampleNormMethodDict = {x: 'NA' for x in refArray['name']}
if not args.gconly:
for i in methodDict:
refSlice = refArray[(refArray['method'] == i)
& (refArray['cells'] == 1)]
methodSamples = [sampleDict[x] for x in refSlice['name']]
methodDict[i] = normalizefile.runMakeMethodRef(
args.species, methodSamples, i, lowessDir)
if methodDict[i][0] != False:
for j in refSlice['name']:
sampleNormMethodDict[j] = i
#run multiprocessing for gc (+ method) correction
normArgs = [
(args.species, sampleDict[x], methodDict[sampleNormMethodDict[x]],
lowessDir + x + '.lowess.txt') for x in sampleDict.keys()
]
common.daemon(normalizefile.runNormalizeOne, normArgs,
'normalize bincount files')
print('\nNormalization complete\n\n\n')
#Run CBS for all samples#
if not args.normalizeonly:
segArgs = [(x, args.species, tempDir, lowessDir, segmentDir)
for x in refArray['name']]
common.daemon(segmentfile.segmentOne, segArgs, 'segment bincount data')
shutil.rmtree(tempDir[:-1])
print('\nSegmentation complete\n\n\n')
def runAll(args):
print('\n\n\nYou have requested to analyze CNV call data')
print('\tWARNING:')
print(
'\t\tIF USING ANY REFERENCES OTHER THAN THOSE I PROVIDE I CANNOT GUARANTEE RESULT ACCURACY'
)
print('\n')
#Set up environment#
args.AnalysisDirectory = common.fixDirName(args.AnalysisDirectory)
folderDict = {
'LowessBinCounts': args.lowess,
'Segments': args.segments,
'PipelineStats': args.countstats
}
for i in list(folderDict.keys()):
if not folderDict[i]:
folderDict[i] = args.AnalysisDirectory + i + '/'
else:
folderDict[i] = common.fixDirName(folderDict[i])
QCdir = args.AnalysisDirectory + 'QC/'
CNVdir = args.AnalysisDirectory + 'CNVlists/'
summaryDir = args.AnalysisDirectory + 'SummaryFiles/'
PloidyPlotDir = args.AnalysisDirectory + 'PloidyDeterminationPlots/'
CNplotDir = args.AnalysisDirectory + 'CopyNumberProfilePlots/'
ChromPlotDir = args.AnalysisDirectory + 'ChromosomeCopyNumberPlots/'
for i in [
args.AnalysisDirectory, QCdir, CNVdir, summaryDir, PloidyPlotDir,
CNplotDir, ChromPlotDir
]: #
common.makeDir(i)
#get list of samples to process
#will involve checking infofile (if present) and whether required input files exist
sampleFiles = common.getSampleList(folderDict['Segments'], args.samples,
'segments')
sampleNames = [x.split('/')[-1].split('.')[0] for x in sampleFiles]
# info = common.importInfoFile(args.infofile, args.columns, 'interpret')
# if args.infofile:
# refArray = info
# else:
# thisDtype = info
# refArray = np.array(
# [ (x, 1, 'unk',) for x in sampleNames],
# dtype=thisDtype)
#QC assessment#
# qcfile.runQCone(sampleNames[0], args.species, folderDict['PipelineStats'], folderDict['LowessBinCounts'], folderDict['Segments'], QCdir, PloidyPlotDir)
argList = [(x, args.species, folderDict['PipelineStats'],
folderDict['LowessBinCounts'], folderDict['Segments'], QCdir,
PloidyPlotDir) for x in sampleNames]
common.daemon(qcfile.runQCone, argList, 'assess sample quality')
analysisSamples = []
ploidyDict = {}
genderDict = {}
mergeQCfile = summaryDir + 'QCmetrics.txt'
OUT = open(mergeQCfile, 'w')
OUT.write('Name\tReads\tMAPD\tCS\tPloidy\tGender\tPASS\n')
for i in sampleNames:
IN = open(QCdir + i + '.qcTEMP.txt', 'r')
data = IN.readline()
OUT.write(data)
data = data.rstrip().split('\t')
if data[-1] == 'True':
analysisSamples.append(i)
ploidyDict[i] = float(data[4])
genderDict[i] = data[-2]
IN.close()
os.remove(QCdir + i + '.qcTEMP.txt')
OUT.close()
os.rmdir(QCdir)
#FUnC: CNV filtering#
if args.nofilter:
print '\nFURTHER CODE IS ONLY DEVELOPED FOR WHEN FUnC IS IMPLEMENTED, EXITING NOW\n\n\n'
raise SystemExit
# funcfile.FUnCone(analysisSamples[0], args.species, folderDict['Segments'], CNVdir,
# ploidyDict[analysisSamples[0]], genderDict[analysisSamples[0]])
argList = [(x, args.species, folderDict['Segments'], CNVdir, ploidyDict[x],
genderDict[x]) for x in analysisSamples]
common.daemon(funcfile.FUnCone, argList, 'remove unreliable CNV calls')
#CNV analysis#
# summaryStats = analyzefiles.analyzeOne(analysisSamples[0], args.species, CNVdir, folderDict['LowessBinCounts'], CNplotDir, ChromPlotDir, ploidyDict[analysisSamples[0]], genderDict[analysisSamples[0]])
# summaryStats = [summaryStats]
argList = [(x, args.species, CNVdir, folderDict['LowessBinCounts'],
CNplotDir, ChromPlotDir, ploidyDict[x], genderDict[x])
for x in analysisSamples]
summaryStats = common.daemon(analyzefiles.analyzeOne, argList,
'create summary files')
cellStatsFile = summaryDir + 'CellStats.txt'
chromAmpFile = summaryDir + 'ChromosomeAmplifiedPercent.txt'
chromDelFile = summaryDir + 'ChromosomeDeletedPercent.txt'
#write summary statistics files#
with open(cellStatsFile,
'w') as CELL, open(chromAmpFile,
'w') as AMP, open(chromDelFile, 'w') as DEL:
CELL.write(
'Sample\tDeletionNumber\tAmplificationNumber\tTotalCNVnumber\tDeletedMB\tAmplifiedMB\tNetDNAalterdMB\n'
)
chromHeader = 'Sample\t' + '\t'.join(summaryStats[0]['chroms']) + '\n'
AMP.write(chromHeader)
DEL.write(chromHeader)
for i, j in enumerate(analysisSamples):
CELL.write(str(j + '\t'))
cellOut = [
summaryStats[i]['cellStats']['delCount'],
summaryStats[i]['cellStats']['ampCount'],
summaryStats[i]['cellStats']['delCount'] +
summaryStats[i]['cellStats']['ampCount'],
np.round(summaryStats[i]['cellStats']['delMB'], 3),
np.round(summaryStats[i]['cellStats']['ampMB'], 3),
np.round(
summaryStats[i]['cellStats']['ampMB'] -
summaryStats[i]['cellStats']['delMB'], 3)
]
cellOut = '\t'.join(map(str, cellOut)) + '\n'
CELL.write(cellOut)
AMP.write(str(j + '\t'))
ampOut = [
np.round(summaryStats[i]['chromAmp'][x], 3)
for x in summaryStats[0]['chroms']
]
ampOut = '\t'.join(map(str, ampOut)) + '\n'
AMP.write(ampOut)
DEL.write(str(j + '\t'))
delOut = [
np.round(summaryStats[i]['chromDel'][x], 3)
for x in summaryStats[0]['chroms']
]
delOut = '\t'.join(map(str, delOut)) + '\n'
DEL.write(delOut)
print('\nCNV analysis complete\n\n\n')