def getOrganismsColors(project):
'''
Check the colors assigned to the organisms and return a dictionary
If no colors are assigned, they are assigned automatically
'''
organism = Organism(project)
colors = {}
for org in organism.getAll():
if not org.color or org.color == '':
colors[org.org_id] = None
else:
colors[org.org_id] = org.color
orgs = colors.keys()
for org, color in colors.iteritems():
# Automatic assignment, probably not the best choiche
# if we got some organism assigned and some others not
if not color:
autocolor = plt.get_cmap('jet')(float( orgs.index(org) )/(len(orgs)-1))
autocolor = pltcls.rgb2hex(autocolor)
colors[org] = autocolor
organism.setColor(org, autocolor)
logger.info('Automatically assigned color to %s'%org)
return colors
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 dClear(project):
'''
Clear all the organisms data
'''
org = Organism(project)
org.delAllOrgs(True)
logger.info('Successfully removed all organisms data')
return True
def dGenomeRemove(project, organisms):
'''
Remove all the genomic data about specific organism ID(s)
'''
gen = Genome(project)
oCheck = Organism(project)
for org in organisms:
if not oCheck.isOrg(org):
logger.warning('Genome %s is not present: skipping'%org)
continue
gen.delProteome(org)
logger.info('Successfully removed genome %s'%org)
return True
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 dRemove(project, organisms):
'''
Remove all the organism info regarding a particular organism ID(s)
'''
org = Organism(project)
for orgID in organisms:
if not org.isOrg(orgID):
logger.warning('Organism %s is not present: skipping'%orgID)
continue
muts = [mutID for mutID in org.getOrgMutants(orgID)]
org.delOrg(orgID, True)
logger.info('Successfully removed organism %s'%orgID)
if len(muts) > 0:
logger.info('Removed also %d %s mutant(s)'%(len(muts),orgID))
return True
def dGenomeMutAdd(project, mutID, mutfasta):
'''
Check and add a mutant
'''
if not os.path.exists(mutfasta):
logger.error('Fasta file %s may not be present'%(mutfasta))
return False
org = Organism(project)
if not org.isOrg(mutID):
logger.warning('Organism %s is not present yet!'%mutID)
return False
gen = Genome(project)
gen.addProteome(mutID, mutfasta)
logger.info('Mutant %s (%s) added, having %d mutated genes'
%(mutID, org.getOrg(mutID).mkind,gen.howMany(mutID)))
return True
def dGenomeAdd(project, orgID, filename):
'''
Add a single genome
'''
if not os.path.exists(filename):
logger.error('Fasta file %s may not be present'%(filename))
return False
filename = os.path.abspath(filename)
org = Organism(project)
if not org.isOrg(orgID):
logger.warning('Organism %s is not present yet!'%orgID)
return False
gen = Genome(project)
gen.addProteome(orgID, filename)
logger.info('Added genome %s, having %d proteins'%
(orgID, gen.howMany(orgID)))
return True
def dGenomeDirAdd(project, folder, extension):
'''
Add a series of genomes contained in a directory
'''
if not os.path.exists(folder):
logger.error('Fasta folder %s may not be present'%(folder))
return False
logger.info('Looking for files with extension %s'%extension)
org = Organism(project)
added = 0
for infile in os.listdir(folder):
if infile.split('.')[-1] != extension:
logger.debug('Skipping file %s'%infile)
continue
orgID = infile.split('.')[0]
filename = os.path.join(folder, infile)
if os.path.isdir(filename):
continue
if not org.isOrg(orgID):
logger.warning('Organism %s is not present yet! Skipping...'%orgID)
continue
if not org.isMutant(orgID):
if not dGenomeAdd(project, orgID, filename):
logger.error('Could not add genome %s'%infile)
return False
else:
if not dGenomeMutAdd(project, orgID, filename):
logger.error('Could not add genome %s'%infile)
return False
added += 1
if added > 0:
logger.info('Added %d genomes from %s'%
(added, folder))
else:
logger.warning('No genomes were added from %s'%folder)
return True
def dAdd(project, orgID, name='', descr='', color=None):
'''
Add a single organism
'''
org = Organism(project)
# If trying to override a present organism, throw an error
if org.isOrg(orgID):
logger.warning('Organism %s is already present'%orgID)
logger.warning('Remove it before addition')
return False
if not color:
org.addOrg(orgID, name=name, description=descr)
else:
org.addOrg(orgID, name=name, description=descr, color=color)
logger.info('Added organism %s'%orgID)
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'
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
def dGenomeExport(project):
# Is there something to be exported?
organism = Organism(project)
if organism.howMany() == 0:
logger.info('No genomic data can be exported at this time')
return False
else:
logger.info('Exporting protein data')
genome = Genome(project)
for org in organism.getAll():
nprots = SeqIO.write([x for x in genome.getRecords(org.org_id)],
open('%s.faa'%org.org_id,'w'), 'fasta')
logger.info('Saved %d proteins from %s (%s)'%(nprots,
org.org_id,
'%s.faa'%org.org_id))
logger.info('Exporting Kegg data')
logger.info('Exporting KO map data')
kegg = Kegg(project)
for org in organism.getAll():
fname = 'ko_%s.tsv'%org.org_id
fout = open(fname,'w')
i = 0
for prot_id, ko_id in kegg.getAllKO(org.org_id):
fout.write('%s\t%s\n'%(prot_id, ko_id.lstrip('ko:')))
i += 1
fout.close()
if i == 0:
os.remove(fname)
logger.warning('No KO links available for %s'%org.org_id)
else:
logger.info('Saved %d KO links for %s (%s)'%(i, org.org_id,
fname))
logger.info('Exporting Kegg reactions data')
for org in organism.getAll():
fname = 'reactions_%s.tsv'%org.org_id
fout = open(fname,'w')
i = 0
for prot_id, re_id in kegg.getAllReactions(org.org_id):
fout.write('%s\t%s\n'%(prot_id, re_id.lstrip('rn:')))
i += 1
fout.close()
if i == 0:
os.remove(fname)
logger.warning('No Kegg reactions available for %s'%org.org_id)
else:
logger.info('Saved %d Kegg reactions links for %s (%s)'%
(i, org.org_id, fname))
proj = Project(project)
if proj.isPanGenome():
logger.info('Exporting pangenome data')
dG = genome.getPanGenome()
if len(dG) == 0:
logger.warning('No pangenome available')
else:
fname = 'pangenome.tsv'
fout = open(fname,'w')
for group, prots in dG.iteritems():
for prot in prots:
fout.write('%s\t%s\n'%(group,prot))
fout.close()
logger.info('Exported %d orthologs (%s)'%(len(dG),fname))
fname = 'pangenome_category.tsv'
fout = open(fname,'w')
dG = genome.getPanGenomeOrgs()
for group in genome.getCore():
fout.write('%s\t%s\t%s\n'%(group.group_id,
'core',
'-'.join(dG[group.group_id])))
for group in genome.getAcc():
fout.write('%s\t%s\t%s\n'%(group.group_id,
'accessory',
'-'.join(dG[group.group_id])))
for group in genome.getUni():
fout.write('%s\t%s\t%s\n'%(group.group_id,
'unique',
'-'.join(dG[group.group_id])))
fout.close()
logger.info('Exported orthologs informations (%s)'%fname)
return True
def dGenomeStats(project, svg=False, doPrint=True):
# Which project are we talking about?
kind = dSetKind(project)
proj = Project(project)
organism = Organism(project)
genome = Genome(project)
kegg = Kegg(project)
if kind == 'single' or kind == 'pangenome':
logger.info('Single genomes stats')
# Single genomes stats
# Header
header = '\t'.join( ['ID', 'name', 'description', 'proteome size',
'mapped to kegg', 'KEGG orthology IDs',
'pathways', 'reactions'] )
if doPrint:
print header
else:
logger.info(header)
lOrg = []
for org in organism.getAll():
org_id = org.org_id
name = org.name if org.name else 'NONE'
description = org.description if org.description else 'NONE'
prots = genome.howMany(org_id)
mapped, ko, react, path = (kegg.howManyMapped(org_id),
kegg.howManyKO(org_id),
kegg.howManyReactions(org_id),
kegg.howManyPathways(org_id))
stats = '\t'.join( [str(x) for x in [org_id, name, description,
prots, mapped, ko, path,
react]] )
if doPrint:
print stats
else:
logger.info(stats)
lOrg.append([org_id, prots, mapped, react])
plotMapBars(lOrg, 'Single genomes statistics', 'single', svg)
if proj.isPanGenome():
logger.info('Pangenome stats')
# Pangenome stats
# Header
header = '\t'.join( ['kind', 'size',
'mapped to kegg', 'KEGG orthology IDs',
'pathways', 'reactions'] )
if doPrint:
print header
else:
logger.info(header)
core, acc, uni = (genome.getLenCore(), genome.getLenAcc(),
genome.getLenUni())
stats = []
stats.append('\t'.join( [str(x) for x in ['core', core,
kegg.howManyMapped(pangenome='core'),
kegg.howManyKO(pangenome='core'),
kegg.howManyPathways(pangenome='core'),
kegg.howManyReactions(pangenome='core')]]))
stats.append('\t'.join( [str(x) for x in ['accessory', acc,
kegg.howManyMapped(pangenome='accessory'),
kegg.howManyKO(pangenome='accessory'),
kegg.howManyPathways(pangenome='accessory'),
kegg.howManyReactions(pangenome='accessory')]]))
stats.append('\t'.join( [str(x) for x in ['unique', uni,
kegg.howManyMapped(pangenome='unique'),
kegg.howManyKO(pangenome='unique'),
kegg.howManyPathways(pangenome='unique'),
kegg.howManyReactions(pangenome='unique')]]))
for stat in stats:
if doPrint:
print stat
else:
logger.info(stat)
lPanGenome = [['Core', core, kegg.howManyMapped(pangenome='core'),
kegg.howManyReactions(pangenome='core')],
['Accessory', acc,
kegg.howManyMapped(pangenome='accessory'),
kegg.howManyReactions(pangenome='accessory')],
['Unique', uni,
kegg.howManyMapped(pangenome='unique'),
kegg.howManyReactions(pangenome='unique')]]
plotMapBars(lPanGenome, 'PanGenome statistics', 'pangenome_stats',
svg)
plotPanGenome(core, acc, uni, svg)
elif kind == 'mutants':
refs = [org.org_id
for org in organism.getAll()
if not organism.isMutant(org.org_id)]
# Header
header = '\t'.join( ['ID', 'name', 'description', 'kind', 'proteome size',
'mapped to kegg', 'reactions'] )
for ref_id in refs:
logger.info('Mutants of %s stats'%ref_id)
if doPrint:
print header
else:
logger.info(header)
muts = [x for x in organism.getOrgMutants(ref_id)]
lOrg = []
for org_id in [ref_id] + muts:
org = organism.getOrg(org_id)
name = org.name if org.name else 'NONE'
description = org.description if org.description else 'NONE'
mkind = org.mkind if org.mkind in ['deletion', 'insertion'] else 'wild-type'
if mkind not in ['deletion', 'insertion']:
prots = genome.howMany(org_id)
elif mkind == 'deletion':
prots = genome.howMany(ref_id) - genome.howMany(org_id)
elif mkind == 'insertion':
prots = genome.howMany(ref_id) + genome.howMany(org_id)
mapped, react = (kegg.howManyMapped(org_id),
kegg.howManyReactions(org_id))
if mkind == 'deletion':
mapped = kegg.howManyMapped(ref_id) - mapped
react = kegg.howManyReactions(ref_id) - react
elif mkind == 'insertion':
mapped += kegg.howManyMapped(ref_id)
react += kegg.howManyReactions(ref_id)
stats = '\t'.join( [str(x) for x in [org_id, name, description,
mkind, prots, mapped,
react]] )
if doPrint:
print stats
else:
logger.info(stats)
lOrg.append([org_id, prots, mapped, react])
plotMapBars(lOrg, 'Wild-type (%s) and mutants statistics'%ref_id,
'%s'%ref_id, svg)
else:
logger.info('No statistics can be computed at this time')
return False
return True
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
