def dPhenomeRemove(project, organisms):
'''
Remove all the phenomic data about specific organism ID(s)
'''
biolog = Biolog(project)
oCheck = Organism(project)
for org in organisms:
if not oCheck.isOrg(org):
logger.warning('Phenome %s is not present: skipping'%org)
continue
biolog.delOrg(org)
logger.info('Successfully removed phenome %s'%org)
if biolog.atLeastOneParameter():
logger.warning('The activity must be recalculated')
return True
def dPhenomeZero(project, blankfile=None):
'''
Takes all the biolog data available and performs the signals zero subtraction
If blankfile is provided, "blank plates" are parsed and then may be used
for zero subtraction
'''
if blankfile:
logger.info('Going to use a blank file for zero subtraction')
if not os.path.exists(blankfile):
logger.error('Blank file %s may not be present'%(blankfile))
return False
bparser = BiologParser(blankfile)
bparser.parse()
if len(bparser.plates) == 0:
logger.warning('The blank file contains no plates!')
return False
biolog = Biolog(project)
# Fetch the signals to be subtracted, then convert them
# to appropriate objects
sigs = [s for s in biolog.getZeroSubtractableSignals()]
plates = []
discarded = set()
for p in getSinglePlates(sigs):
if p.plate_id in zeroPlates:
if blankfile:
for zp in bparser.plates:
if zp.plate_id == p.plate_id:
plates.append(p)
else:
plates.append(p)
else:
discarded.add(p.plate_id)
if len(plates) == 0:
logger.warning('No plates can be zero subtracted!')
logger.warning('Found these plates: %s'%' '.join(discarded))
return False
if blankfile:
zsub = BiologZero(plates, blank = True, blankData=bparser.plates)
else:
zsub = BiologZero(plates)
if not zsub.zeroSubTract():
logger.warning('Zero subtraction failed!')
return False
# Grep the wells
wells = [w for plate in zsub.plates for w in plate.getWells()]
# Add to the project
biolog = Biolog(project)
biolog.addWells(wells, clustered=False)
logger.info('Zero subtraction done on %d plates'%len(plates))
if biolog.atLeastOneParameter():
logger.warning('The activity must be recalculated')
return True
