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'
def dGetGenomeSteps(project):
'''
Get the analysis that these genomes deserve
'''
proj = Project(project)
proj.getProject()
status = proj.genome
pangenome = bool(proj.pangenome)
kind = dSetKind(project)
if kind == 'mutants':
if status == 'map2ko':
return ['map2kegg']
elif status == 'map2kegg':
return []
else:
return ['map2ko', 'map2kegg']
elif kind == 'single':
if status == 'map2ko':
return ['map2kegg']
elif status == 'map2kegg':
return []
else:
return ['map2ko', 'map2kegg']
else:
steps = []
if not pangenome:
steps.append('pangenome')
if status == 'map2ko':
steps.append('map2kegg')
elif status == 'map2kegg':
pass
else:
steps.append('map2ko')
steps.append('pangenome')
return steps
