def getRepeatForKnownGene(commonOptions, specifiedOptions, moreOptions={}):
if "repeatName" in moreOptions:
repeatName = moreOptions['repeatName'].lower() # repeatName.lower()
else:
repeatName = commonOptions['repeatName'].lower()
moreOptions['repeatName'] = repeatName
retoptions = get_gLoc(repeatName, commonOptions)
mgloc = retoptions['mgloc']
if commonOptions['outlog'] <= M_INFO:
print('mgloc', mgloc)
moreOptions.update(retoptions)
myHMM.produce_for_repPat(commonOptions, moreOptions)
if specifiedOptions["SepbamfileTemp"] is not None:
specifiedOptions["bamfile"] = (specifiedOptions["SepbamfileTemp"] % moreOptions['chr'][3:])
myret = {}
myretdetail = {}
if (commonOptions['SplitAndReAlign'] in [0, 2]) or testall:
start_time = time.time()
if commonOptions['outlog'] <= M_INFO and 'thread' not in specifiedOptions:
print('p2bamhmm start')
p2bamhmm = getRepeatForGivenGene(commonOptions, specifiedOptions, moreOptions)
memres = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024
if p2bamhmm is None:
print('ERROR None detection', moreOptions['repeatName'], mgloc)
logging.error('ERROR None detection: ' +
str(moreOptions['repeatName']) + ' ' + str(mgloc))
else:
addSumForAGene(p2bamhmm, myret, myretdetail, 'p2bamhmm', 2)
end_time = time.time()
if commonOptions['outlog'] <= M_WARNING and 'thread' not in specifiedOptions:
print('p2bamhmm end---running time%.0f mem%d' % (end_time - start_time, memres))
sys.stdout.flush()
if (commonOptions['SplitAndReAlign'] in [1, 2]) or testall:
start_time = time.time()
if commonOptions['outlog'] <= M_INFO and 'thread' not in specifiedOptions:
print('p2sp start')
moreOptions['fafqfile'] = specifiedOptions["bamfile"]
moreOptions['fafqtype'] = 'bam'
p2sp = myRepeatReAlignment.getRepeatCounts(commonOptions, specifiedOptions, moreOptions)
memres = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024
if p2sp is None:
print('ERROR None detection (sp)', moreOptions['repeatName'], mgloc)
logging.error('ERROR None detection (sp): ' +
str(moreOptions['repeatName']) + ' ' + str(mgloc))
else:
addSumForAGene(p2sp, myret, myretdetail, 'p2sp', 2)
end_time = time.time()
if commonOptions['outlog'] <= M_WARNING and 'thread' not in specifiedOptions:
print('p2sp end---running time%.0f mem%d' % (end_time - start_time, memres))
sys.stdout.flush()
return [myret, myretdetail]
def detectRepCounts(commonOptions, specifiedOptions, moreOptions):
retoptions = myBAMhandler.get_Loc1(moreOptions['mgloc'], commonOptions)
if commonOptions['outlog'] <= M_INFO: print 'mgloc', moreOptions['mgloc']
#print moreOptions['mgloc'][:5]
moreOptions.update(retoptions)
myHMM.produce_for_repPat(commonOptions, moreOptions)
if not specifiedOptions["SepbamfileTemp"]==None:
specifiedOptions["bamfile"] = (specifiedOptions["SepbamfileTemp"] % moreOptions['chr'][3:])
if (commonOptions['SplitAndReAlign'] in [0,2]) or testall:
start_time = time.time();
if commonOptions['outlog'] <= M_INFO and (not specifiedOptions.has_key('thread')): print 'p2bamhmm start'
p2bamhmm = myBAMhandler.getRepeatForGivenGene(commonOptions, specifiedOptions, moreOptions)
memres = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1024
if p2bamhmm==None:
print 'ERROR None detection', moreOptions['repeatName'], moreOptions['mgloc']
logging.error('ERROR None detection: ' + str( moreOptions['repeatName']) + ' ' + str(moreOptions['mgloc']))
else:
addSumForAGene(p2bamhmm, 'p2bamhmm', 2, commonOptions, specifiedOptions, moreOptions)
end_time = time.time();
if commonOptions['outlog'] <= M_WARNING and (not specifiedOptions.has_key('thread')): print ('p2bamhmm end---running time%.0f mem%d' % (end_time-start_time, memres)); sys.stdout.flush()
if (commonOptions['SplitAndReAlign'] in [1,2]) or testall:
start_time = time.time();
if commonOptions['outlog'] <= M_INFO and (not specifiedOptions.has_key('thread')): print 'p2sp start'
moreOptions['fafqfile'] = specifiedOptions["bamfile"]
moreOptions['fafqtype'] = 'bam'
p2sp = myRepeatReAlignment.getRepeatCounts(commonOptions, specifiedOptions, moreOptions)
memres = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1024
if p2sp==None:
print 'ERROR None detection (sp)', moreOptions['repeatName'], moreOptions['mgloc']
logging.error('ERROR None detection (sp): ' + str( moreOptions['repeatName']) + ' ' + str(moreOptions['mgloc']))
else:
addSumForAGene(p2sp, 'p2sp', 2, commonOptions, specifiedOptions, moreOptions)
end_time = time.time();
if commonOptions['outlog'] <= M_WARNING and (not specifiedOptions.has_key('thread')): print ('p2sp end---running time%.0f mem%d' % (end_time-start_time, memres)); sys.stdout.flush()
def getSCA3ForGivenGene(commonOptions, specifiedOptions, moreOptions):
predres = []
mgloc = moreOptions['mgloc']
repeatName = moreOptions['repeatName']
gene_start_end = moreOptions['gene_start_end']
repeat_start_end = moreOptions['repeat_start_end']
fastafile = specifiedOptions['fastafile']
unique_file_id = specifiedOptions['unique_file_id']
analysis_file_id = specifiedOptions['analysis_file_id']
hgfile = commonOptions['hgfile']
MinSup = commonOptions['MinSup']
repPat = moreOptions['repPat']
myHMM.produce_for_repPat(commonOptions, moreOptions)
len_repPat = printHMMmatrix.get_len_repPat(repPat, commonOptions)
logging.info("len_repPat=" + str(len_repPat))
repPat = moreOptions['repPat']
upstreamstr, repregion, downstreamstr = get3part(
mgloc, gene_start_end, repeat_start_end, repeatName, unique_file_id,
analysis_file_id, hgfile, specifiedOptions)
if len(repregion) == 0:
logging.error("Not repeat region! please check!!" + repeatName +
(' gene_location=[%d, %d], repeat_location=[%d, %d]' %
(gene_start_end[0], gene_start_end[1],
repeat_start_end[0], repeat_start_end[1])))
sys.exit(1)
logging.info("Test " + repeatName + (
' gene_location=[%d, %d], repeat_location=[%d, %d]; upstreamsize=%d, downstreamsize=%d'
% (gene_start_end[0], gene_start_end[1], repeat_start_end[0],
repeat_start_end[1], repeat_start_end[0] - gene_start_end[0],
gene_start_end[1] - repeat_start_end[1])))
logging.info("Normal/Pathogenic repeats: %s" % mgloc[5])
orirepeat = int(len(repregion) / float(len_repPat)) #3)
logging.info("Orignal Test read=" + '<<<' + repregion + '>>>' +
(" #repeat=%d; #len=%d" % (orirepeat, len(repregion))))
bwamem_w_option = 90 * 4
max_w_option, min_w_option = 500, 100
if bwamem_w_option < min_w_option: bwamem_w_option = min_w_option
if bwamem_w_option > max_w_option: bwamem_w_option = max_w_option
bwamem_w_option = bwamem_w_option + int(
len(upstreamstr + repregion + downstreamstr) * 0.4)
if bwamem_w_option > max_w_option: bwamem_w_option = max_w_option
start_time = time.time()
bamfile = fastafile + '.bam'
bamfile = fastafile + unique_file_id + '.bam'
specifiedOptions['bamfile'] = bamfile
myret = {}
myretdetail = {}
#cmd = 'bwa mem -k17 -w'+str(bwamem_w_option)+' -W40 -r10 -A1 -B1 -O1 -E1 -L1 -t '+mthreads+' -v 2 '+hg_reference_and_index+'/'+hgfile+' '+ fastafile +' | samtools view -S -b | samtools sort > '+bamfile
cmd = 'bwa mem -k17 -w' + str(
bwamem_w_option
) + ' -W40 -r10 -A1 -B1 -O1 -E1 -L1 -t ' + mthreads + ' -v 2 ' + hgfile + ' ' + fastafile + ' | samtools view -S -b | samtools sort > ' + bamfile
logging.info(cmd)
os.system(cmd)
cmd = 'samtools index ' + bamfile
logging.info(cmd)
os.system(cmd)
if (commonOptions['SplitAndReAlign'] in [0, 2]) or testall:
start_time = time.time()
if commonOptions['outlog'] <= M_INFO and (
not specifiedOptions.has_key('thread')):
print 'p2bamhmm start'
sys.stdout.flush()
p2bamhmm = myBAMhandler.getRepeatForGivenGene(commonOptions,
specifiedOptions,
moreOptions)
memres = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024
if p2bamhmm == None:
print 'ERROR None detection', moreOptions['repeatName'], mgloc
logging.error('ERROR None detection: ' +
str(moreOptions['repeatName']) + ' ' + str(mgloc))
else:
myBAMhandler.addSumForAGene(p2bamhmm, myret, myretdetail,
'p2bamhmm', 2)
end_time = time.time()
if commonOptions['outlog'] <= M_WARNING and (
not specifiedOptions.has_key('thread')):
print('p2bamhmm end---running time%.0f mem%d' %
(end_time - start_time, memres))
sys.stdout.flush()
if (commonOptions['SplitAndReAlign'] in [1, 2]) or testall:
start_time = time.time()
if commonOptions['outlog'] <= M_INFO and (
not specifiedOptions.has_key('thread')):
print 'start p2sp'
sys.stdout.flush()
#moreOptions['fafqfile'] = specifiedOptions['fastafile']
#moreOptions['fafqtype'] = 'fq'
moreOptions['fafqfile'] = bamfile
moreOptions['fafqtype'] = 'bam'
p2sp = myRepeatReAlignment.getRepeatCounts(commonOptions,
specifiedOptions,
moreOptions)
memres = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024
if p2sp == None:
print 'ERROR None detection (sp)', moreOptions['repeatName'], mgloc
logging.error('ERROR None detection (sp): ' +
str(moreOptions['repeatName']) + ' ' + str(mgloc))
else:
myBAMhandler.addSumForAGene(p2sp, myret, myretdetail, 'p2sp', 2)
end_time = time.time()
if commonOptions['outlog'] <= M_WARNING and (
not specifiedOptions.has_key('thread')):
print('p2sp end---running time%.0f mem%d' %
(end_time - start_time, memres))
sys.stdout.flush()
os.system('rm ' + bamfile)
os.system('rm ' + bamfile + '.bai')
return [myret, myretdetail]