def correlate(args):
force = args.force
tool = args.wig_tool
db_file = args.db_file
db = chipqc_db.ChipQcDbSqlite(path=db_file)
limit = -1
if 'limit' in args and args.limit != None:
limit = args.limit
## Find required Correlation to run
corrList = list()
if 'correlation_id' in args and args.correlation_id != None:
corrList.append(args.correlation_id)
corrList = _loadSelectedJobs(db,
force=force,
correlations=corrList,
limit=limit)
else:
corrList = _loadJobList(db, force=force, limit=limit)
print "Processing %s jobs ..." % (len(corrList))
reslist = _processJobs(tool, corrList,
lambda id, y: _storeValue(db, id, y), executeCmd)
def run(parser, args):
db_file = args.db_file
db = chipqc_db.ChipQcDbSqlite(path=db_file)
if 'fl_file' in args and args.fl_file is not None:
load(db, args.fl_file)
elif 'at_file' in args and args.at_file is not None:
annotateFile(db, args.at_file)
else:
parser.print_help()
def calculate(args):
force = args.force
tool = args.wig_tool
db_file = args.db_file
db = chipqc_db.ChipQcDbSqlite(path=db_file)
col = args.annot_col
out_dir = args.out_dir
if not os.path.exists(out_dir):
os.makedirs(out_dir)
## Find all jobs (based on annotation)
updateDatabase(db, col, out_dir)
## Load all jobs
allJobs = db.getCoverage()
## Find required Jobs to run
jobs = allJobs
limit = -1
if 'limit' in args and args.limit != None:
limit = args.limit
if 'job_id' in args and args.job_id != None:
max_id = args.job_id + 1
if limit > 0:
max_id = args.job_id + limit
jobs = [r for r in jobs if r[0] >= args.job_id and r[0] < max_id]
if args.l_jobs:
printStatus(db, jobs)
return
if args.l_details:
printStatus(db, jobs, details=True)
return
jobs = [r for r in jobs if force or r[3] == 'init'] ## status is init
print "Processing %s jobs ..." % (len(jobs))
## Build commands
cmdIdx = _createCommandIdx(
db, tool,
getBedFile(genome=args.genome, prefix=args.chr_exist == "True"), jobs)
## Execute
reslist = map(
lambda id: executeCmd(cmdIdx[id], lambda x: _storeValue(db, id, x)),
cmdIdx.keys())
def run(parser, args):
args.out_dir = os.path.abspath(args.out_dir)
db_file = args.db_file
db = chipqc_db.ChipQcDbSqlite(path=db_file)
if args.skip:
skipFilter(db, args)
elif 'reg_build' not in args or args.reg_build is None:
print("Regulatory build parameter required ")
return 1
else:
ret = filter(db, args)
if ret != 0:
print("Error: there were errors during execution !!!")
return 0
def runScreenshots(args):
db_file = args.db_file
out_dir = args.out_dir
r_file = getRFile()
bed_file = os.path.abspath(args.bed_file)
db = chipqc_db.ChipQcDbSqlite(path=db_file)
if not os.path.exists(out_dir):
os.makedirs(out_dir)
allJobs = db.getFiles()
jobs = allJobs
limit = -1
if 'limit' in args and args.limit != None:
limit = args.limit
if 'job_id' in args and args.job_id != None:
max_id = args.job_id + 1
if limit > 0:
max_id = args.job_id + limit
jobs = [r for r in jobs if r[0] >= args.job_id and r[0] < max_id]
## Print INFO
if args.l_jobs:
printStatus(db, jobs)
return
print "Processing %s jobs ..." % (len(jobs))
## Build commands
cmdIdx = _createCommandIdx(db,
r_file,
out_dir,
bed_file,
jobs,
grch37=args.rel_37)
## Execute
reslist = map(
lambda id: executeCmd(cmdIdx[id], lambda x: _storeValue(db, id, x)),
cmdIdx.keys())
return None
def run(parser, args):
db_file = args.db_file
db = chipqc_db.ChipQcDbSqlite(path=db_file)
if args.f_file:
filterIds(db)
elif args.f_file_detail:
filterDetailsIds(db)
elif args.l_file:
loadedIds(db)
elif args.la_file:
loadedAnnotIds(db)
elif args.c_list:
correlationIds(db)
elif args.C_list:
correlationSampleIds(db)
elif 'detail_id' in args and args.detail_id != None:
correlationDetails(db, args.detail_id)
else:
print "One option required!!!"
parser.print_help()
return 1
return 0
def analyseEnrichment(args):
db_file = args.db_file
force = args.force
out_dir = args.out_dir
col = args.annot_col
countAnnot = args.annot_cnt
r_file = getRFile()
db = chipqc_db.ChipQcDbSqlite(path=db_file)
if not os.path.exists(out_dir):
os.makedirs(out_dir)
## Find all jobs (based on annotation)
updateDatabase(db, col, out_dir)
allJobs = db.getEnrichment()
jobs = allJobs
limit = -1
if 'limit' in args and args.limit != None:
limit = args.limit
if 'job_id' in args and args.job_id != None:
max_id = args.job_id + 1
if limit > 0:
max_id = args.job_id + limit
jobs = [r for r in jobs if r[0] >= args.job_id and r[0] < max_id]
## Print INFO
if args.l_jobs:
printStatus(db, countAnnot, jobs, details=False)
return
elif args.l_details:
printStatus(db, countAnnot, jobs, details=True)
return
jobs = [r for r in jobs if force or r[4] == 'init'] ## status is init
print "Processing %s jobs ..." % (len(jobs))
## Build commands
cmdIdx = _createCommandIdx(db, r_file, countAnnot, jobs)
## Execute
reslist = map(
lambda id: executeCmd(cmdIdx[id], lambda x: _storeValue(db, id, x)),
cmdIdx.keys())
## TODO implement
## Calculate mean value for each BIN (done before
## INPUT
## -> calculate mean
## IP files
## -> calculate mean
##
## wiggletools apply_paste mean.txt meanI regions.chr.bed BW
## execute Enrichment R script to
## -> Plot + result file
## -> read result file and put into DB
# cmdTemplate=" Rscript {0} --db {1} --out {2}"
# cmd=cmdTemplate.format(r_file,db_file,out_dir)
# res = execCmd(cmd)
# start=res[0]
# end=res[1]
# exitVal = res[2]
# out = res[3]
# err = res[4]
# print (res)
return None