示例#1
0
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
示例#2
0
def dPhenomeAdd(project, orgID, filename):
    '''
    Add a single phenome
    '''
    if not os.path.exists(filename):
        logger.error('Phenomic file %s may not be present'%(filename))
        return False
    
    org = Organism(project)
    if not org.isOrg(orgID):
        logger.warning('Organism %s is not present yet!'%orgID)
        return False
    
    filename = os.path.abspath(filename)
    
    bparser = BiologParser(filename)
    bparser.parse()
    
    if len(bparser.plates) == 0:
        logger.warning('No biolog data was found!')
        return False
    
    # Check the organisms id inside the biolog files
    strainNumbers = set([plate.strainNumber for plate in bparser.plates])
    strainNames = set([plate.strainName for plate in bparser.plates])
    samples = set([plate.sample for plate in bparser.plates])
    
    if orgID not in samples:
        logger.debug('No sign of %s in sample field'%orgID)
    if orgID not in strainNames:
        logger.debug('No sign of %s in strainName field'%orgID)
    if orgID not in strainNumbers:
        logger.debug('No sign of %s in strainNumber field'%orgID)
    
    # TODO: regular expression search
    if orgID in samples:
        if len(samples) > 1:
            logger.warning('''More than one organism ID may be present in this phenomic data file!''')
            logger.warning('''%s'''%' '.join(samples))
            return False
        
        for plate in bparser.plates:
            plate.strain = plate.sample
            
    elif orgID in strainNames:
        if len(strainNames) > 1:
            logger.warning('''More than one organism ID may be present in this phenomic data file!''')
            logger.warning('''%s'''%' '.join(strainNames))
            return False
        
        for plate in bparser.plates:
            plate.strain = plate.strainName
        
    elif orgID in strainNumbers:
        if len(strainNumbers) > 1:
            logger.warning('''More than one organism ID may be present in this phenomic data file!''')
            logger.warning('''%s'''%' '.join(strainNumbers))
            return False
        
        for plate in bparser.plates:
            plate.strain = plate.strainNumber
        
    else:
        logger.warning('''The organism ID you provided was not found inside the phenomic data file''')
        logger.info('''Using it anyway to add this data''')
    
    # Prepare a series of Plate objects to catch the replicas
    dPlates={}
    for plate in bparser.plates:
        if plate.plate_id not in dPlates:
            dPlates[plate.plate_id] = Plate(plate.plate_id)
        dPlates[plate.plate_id].addData(plate.strain, plate)
    
    # Grep the wells
    wells = [w for plate in dPlates.itervalues() for w in plate.getWells()]
    
    # Add to the project
    biolog = Biolog(project)
    biolog.addWells(wells, clustered=False)
    
    logger.info('Added phenome %s, having %d biolog plates (%d wells)'%
                (orgID, len(dPlates), len(wells)))
    
    return True
示例#3
0
def dPhenomeMultiAdd(project, filename):
    '''
    Add a single phenomic file with multiple organisms in it
    '''
    if not os.path.exists(filename):
        logger.error('Phenomic file %s may not be present'%(filename))
        return False
    
    filename = os.path.abspath(filename)
    
    bparser = BiologParser(filename)
    bparser.parse()
    
    if len(bparser.plates) == 0:
        logger.warning('No biolog data was found!')
        return False
    
    # Check the organism ids inside the biolog files
    # Assuming the names are correct AND stored inside the strainName field
    logger.debug('Assuming organism IDs are correct and inside the field strainName')
    strainNames = set([plate.strainName for plate in bparser.plates])
    
    strainNames.discard(None)
    strainNames.discard('')
    
    if len(strainNames) == 0:
        logger.warning('''Field strainName doesn't contain any value (%s)'''%filename)
        return False
        
    logger.info('Found the following organism IDs: %s'%' '.join(strainNames))
    
    for plate in bparser.plates:
        plate.strain = plate.strainName
    
    # TODO: regular expressions verification
    
    orgs = strainNames
    
    for orgID in orgs:
        org = Organism(project)
        if not org.isOrg(orgID):
            logger.warning('Organism %s is not present yet! Skipping...'%orgID)
            continue
        
        # Prepare a series of Plate objects to catch the replicas
        dPlates={}
        for plate in bparser.plates:
            if plate.strain == orgID:
                if plate.plate_id not in dPlates:
                    dPlates[plate.plate_id] = Plate(plate.plate_id)
                dPlates[plate.plate_id].addData(plate.strain, plate)
        
        # Grep the wells
        wells = [w for plate in dPlates.itervalues() 
                 for w in plate.getWells()]
        
        # Add to the project
        biolog = Biolog(project)
        biolog.addWells(wells, clustered=False)
        
        logger.info('Added phenome %s, having %d biolog plates (%d wells)'%
                    (orgID, len(dPlates), len(wells)))
    
    return True