def dMutAdd(project, mutID, mutparent,kind, name='', descr='', color=None):
'''
Check and add a mutant
'''
org = Organism(project)
if org.isOrg(mutID):
logger.warning('Organism %s is already present'%mutID)
logger.warning('Remove it before addition')
return False
if not org.isOrg(mutparent):
logger.error('Parent organism %s not present!'%mutparent)
return False
elif org.isMutant(mutparent):
logger.error('Parent organism %s cannot be a mutant!'%mutparent)
return False
parents = len(org) - org.howManyMutants()
if parents != 1:
logger.error('Only one parent is allowed!')
return False
if not color:
org.addOrg(mutID, name=name, description=descr,
mutant=True, reference=mutparent, mkind=kind)
else:
org.addOrg(mutID, name=name, description=descr,
mutant=True, reference=mutparent, mkind=kind, color=color)
logger.info('Mutant %s (%s) added'
%(mutID, org.getOrg(mutID).mkind))
return True
def dSetKind(project):
'''
Set the kind of genomic project and return its value
'''
proj = Project(project)
proj.getProject()
org = Organism(project)
if org.howManyMutants() > 0:
logger.info('%d mutants are present'%org.howManyMutants())
proj.setKind('mutants')
return 'mutants'
elif org.howMany() == 1:
logger.info('Just one organism is present')
proj.setKind('single')
return 'single'
elif org.howMany() == 0:
logger.info('No organisms are present yet')
return None
else:
logger.info('%d organisms are present'%org.howMany())
proj.setKind('pangenome')
return 'pangenome'