def RunPipeline(**kwargs):
setGroup = set()
"""
listSamples is ...
190819_Nahye_12K_D4_D0_1-Cas9D7 Cas9D7 Ctrl
190819_Nahye_12K_D4_eCas9_Rep1-Cas9D7 Cas9D7 Exp ...
"""
for strSample in listSamples:
"""
tupSampleInfo is ... tuple instance
(190819_Nahye_12K_D4_D0_1-Cas9D7, Cas9D7, Ctrl)
"""
tupSampleInfo = Helper.SplitSampleInfo(strSample)
if not tupSampleInfo: continue
"""
strSample = 190819_Nahye_12K_D4_D0_1-Cas9D7 ... sample name
, strRef = Cas9D7 ... reference name
, strExpCtrl = Ctrl/Exp/""
"""
strSample, strRef, strExpCtrl = tupSampleInfo
setGroup.add(strExpCtrl)
"""
options ... has PAM type: Cas9 Cpf1, PAM position: Forward Reverse ...
"""
InstRunner = clsIndelSearcherRunner(strSample, strRef, options, InstInitFolder)
#"""
logging.info('SplitFile')
InstRunner.SplitFile()
logging.info('MakeReference')
InstRunner.MakeReference()
"""
Indel_searcher_crispresso_hash.py
"""
logging.info('MakeIndelSearcherCmd')
listCmd = InstRunner.MakeIndelSearcherCmd()
logging.info('RunMulticore')
RunMulticore(listCmd, options.multicore) ## from CoreSystem.py
logging.info('MakeOutput')
InstRunner.MakeOutput()
logging.info('RunIndelFreqCalculator')
InstRunner.RunIndelFreqCalculator()
#"""
if setGroup == {'EXP', 'CTRL'}:
InstRunner.IndelNormalization()
elif setGroup in [set(), set([]), set(['']), set([' '])]:
pass
else:
logging.error('The group category is not appropriate. : %s' % setGroup)
logging.error('Please make sure your project file is correct.')
logging.error('The group category must be Exp or Ctrl')
raise Exception
def RunPipeline(**kwargs):
for strSample in listSamples:
if strSample[0] == '#': continue
tupSampleInfo = Helper.SplitSampleInfo(strSample)
if not tupSampleInfo: continue
strSample, strRef, strExpCtrl = tupSampleInfo
InstBaseEdit = clsBaseEditRunner(strSample, strRef, options,
InstInitFolder)
InstBaseEdit.MakeReference()
listCmd = InstBaseEdit.MakeIndelSearcherCmd()
###print(lCmd[:5])
RunMulticore(listCmd, options.multicore) ## from CoreSystem.py
InstBaseEdit.MakeMergeTarget()
InstBaseEdit.CopyToAllResultFolder()
def Main():
logging.info('Program Start')
logging.info('Make commands for a multiple processing')
lPara = []
with open('./User/{user}/{project}.txt'.format(
user=strUser, project=strProject)) as Project_list:
for strSample in Project_list:
if strSample[0] == '#': continue
tupSampleInfo = Helper.SplitSampleInfo(strSample)
if not tupSampleInfo: continue
strSample, strRef, strExpCtrl = tupSampleInfo
strSample = strSample.replace('\n', '').replace('\r', '')
sFile_path = './Output/{user}/{project}/{sample}/Tmp/Alignment'.format(
user=strUser, project=strProject, sample=strSample)
sTotal_readcnt_path = './Output/{user}/{project}/{sample}/Tmp/All'.format(
user=strUser, project=strProject, sample=strSample)
dInput_fa = Make_ref_dict(strRef)
lPara.append(
[strSample, sFile_path, sTotal_readcnt_path, dInput_fa])
logging.info('Multiple processing Start')
p = mp.Pool(iCore)
p.map_async(Count_seq_freq, lPara).get()
logging.info('Multiple processing End')
#logging.info('Count group Start')
#Count_group()
#logging.info('Count group End')
#logging.info('Trim data Start')
#Trim_data()
#logging.info('Trim data End')
logging.info('Program End')
def RunPipeline(**kwargs):
setGroup = set()
for strSample in listSamples:
tupSampleInfo = Helper.SplitSampleInfo(strSample)
if not tupSampleInfo: continue
strSample, strRef, strExpCtrl = tupSampleInfo
setGroup.add(strExpCtrl)
InstRunner = clsIndelSearcherRunner(strSample, strRef, options,
InstInitFolder)
#"""
logging.info('SplitFile')
InstRunner.SplitFile()
logging.info('MakeReference')
InstRunner.MakeReference()
logging.info('MakeIndelSearcherCmd')
listCmd = InstRunner.MakeIndelSearcherCmd()
logging.info('RunMulticore')
RunMulticore(listCmd, options.multicore) ## from CoreSystem.py
logging.info('MakeOutput')
InstRunner.MakeOutput()
logging.info('RunIndelFreqCalculator')
InstRunner.RunIndelFreqCalculator()
#"""
if setGroup == {'EXP', 'CTRL'}:
InstRunner.IndelNormalization()
elif setGroup in [set(), set([]), set(['']), set([' '])]:
pass
else:
logging.error('The group category is not appropriate. : %s' %
setGroup)
logging.error('Please make sure your project file is correct.')
logging.error('The group category must be Exp or Ctrl')
raise Exception