def processSampleFromLibarary(sampleID, sampleIDList, libraryBamFileList):
''''''
########################## 0. init #########################
#__init__(self, sampleName, outdir, fq1, fq2='', qualityBase='33', cfgfile='~/.NGSTools.cfg')
mySample = NGSTools.NGSTools(sampleID,
args.outDir,
fq1=sampleIDList[0],
fq2=sampleIDList[1],
qualityBase=args.qbase,
cfgfile=os.path.abspath(args.config))
########################## 1. QC #########################
if QC:
mySample.cutadapter(run=_run)
mySample.QC_fastqc(run=_run)
########################## 2. Mapping #######################
if BWA:
finalBam = mySample.bwa(run=_run)
#finalBam = mySample.bowtie2(mode='--end-to-end', run=_run)
finalBam = mySample.samtools_sort(run=_run)
libraryBamFileList.append(finalBam)
def processSampleFromLibarary(sampleID, sampleIDList, libraryBamFileList):
''''''
########################## 0. init #########################
#__init__(self, sampleName, outdir, fq1, fq2='', quanlityBase='33', cfgfile='~/.NGSTools.cfg')
mySample = NGSTools.NGSTools(sampleID,
args.outDir,
fq1=sampleIDList[0],
fq2=sampleIDList[1],
cfgfile=os.path.abspath(args.config))
########################## 1. QC #########################
if QC:
mySample.trim_Galore(args.rrbs, run=_run)
mySample.QC_fastqc(run=_run)
########################## 2. Mapping #######################
if Bismark:
finalBam = mySample.Bismark(run=_run)
elif Bs_seeker2:
finalBam = mySample.Bs_seeker2(run=_run)
else:
print 'WARNING: not choose a mapping tools'
libraryBamFileList.append(finalBam)
def processSample(line, condition, transcripts, countsFiles, finalBam,
expressCXB):
cols = line.strip().split('\t')
if len(cols) == 3:
# single end library
fq2 = '-'
else:
# paired end
fq2 = cols[3]
sample = {
'name': cols[0],
'condition': cols[1],
'fq1': cols[2],
'fq2': fq2,
'bam': ''
}
########################## 0. init #########################
#__init__(self, sampleName, outdir, fq1, fq2='', quanlityBase='32', cfgfile='~/.NGSTools.cfg'):
mySample = NGSTools.NGSTools(sample['name'],
args.outDir,
sample['fq1'],
sample['fq2'],
libType=args.libraryType,
cfgfile=os.path.abspath(args.config))
if QC:
#################### 1. Quality Control ####################
###### 1.1 cut adapter ######
if args.dataType == 'raw':
#mySample.cutadapter(adapter5='', adapter3='AATGATACGGCGACCACCGAGATCT', run = _run)
mySample.cutadapter(run=_run)
### Nextera Kit
#mySample.cutadapter(adapter5='CTGTCTCTTATACAC', adapter3='CTGTCTCTTATACAC',run = _run)
#mySample.rm_lowQual(run = _run)
else:
pass
##### 1.2 fastqc #####
mySample.QC_fastqc(run=_run)
if Mapping:
######################## 2. Mapping ########################
sample['bam'] = mySample.tophat2(run=_run)
if condition.has_key(sample['condition']):
#condition[sample['condition']][sample['name']] = sample['bam']
condition[sample['condition']] += "," + sample['bam']
else:
#condition[sample['condition']] = {sample['name'] : sample['bam']}
condition[sample['condition']] = sample['bam']
if GFold:
# GFold count
mySample.gfoldCount(run=_run)
if DESeq:
# DESeq2
count = mySample.HTSeq_count(run=_run)
countsFiles[count] = sample['condition'] + '|' + sample['name']
if GATK:
# remove duplicates
mySample.rmdup(run=_run)
# picard reorder
mySample.picard_reorder(run=_run)
# splitN
mySample.splitN(run=_run)
# realign
realnBam = mySample.realn(run=_run)
# recal need known SNP site
# recal
#recalBam = mySample.recal(run = _run)
finalBam[realnBam] = sample['condition']
# samtools call SNP/InDel
mySample.samtools_call(run=_run)
mySample.samtools_filter(run=_run)
######################## DEGs calling preparation ########################
if Cufflinks:
##### 3. cufflinks #####
cuffdir = os.path.join(args.outDir, 'cufflinks')
if not os.path.exists(cuffdir):
os.mkdir(cuffdir)
# cufflinks #
command = 'cufflinks --library-type %s -p 4 -g %s -o %s %s' % (
args.libraryType, cfg.gtf,
os.path.join(cuffdir, sample['condition'] + '_' + sample['name']),
sample['bam'])
NGSTools.writeCommands(command,
cuffdir + '/cufflinks_%s.sh' % sample['name'],
_run)
transcripts.append(
os.path.join(cuffdir, sample['condition'] + '_' + sample['name'],
'transcripts.gtf'))
