class ProteomeData(MeasurementModel):
locus = dmodels.ForeignKey('Locus', on_delete=models.PROTECT)
fold_change = dmodels.FloatField(di_show=True)
adjusted_p_value = dmodels.FloatField(di_show=True,
validators=[validate_probabilty])
unique_peptides = dmodels.IntegerField()
class Meta:
unique_together = (('locus', 'experiment'), )
verbose_name_plural = 'Proteom data'
def __str__(self):
return 'Proteome Datapoint'
class CoAData(ExperimentalData):
co_a_derivative = dmodels.ForeignKey('CoADerivative',
on_delete=models.PROTECT)
stderr = dmodels.FloatField(null=True, blank=True, di_show=True)
class Meta:
unique_together = (('co_a_derivative', 'experiment'), )
verbose_name_plural = 'CoA data'
def __str__(self):
return 'CoA datapoint'
class FluxData(MeasurementModel):
flux = dmodels.FloatField(di_show=True, validators=[validate_flux])
flux_min = dmodels.FloatField(di_show=True,
di_display_name='lb',
validators=[validate_flux])
flux_max = dmodels.FloatField(di_show=True,
di_display_name='ub',
validators=[validate_flux])
reaction = dmodels.ForeignKey('Reaction', on_delete=models.CASCADE)
class Meta:
unique_together = ((
'reaction',
'experiment',
))
verbose_name_plural = 'Fluxes'
def __str__(self):
return 'Flux datapoint'
class Reaction(BiologicalModel):
name = dmodels.CharField(max_length=255,
unique=True,
di_show=True,
di_display_name='reaction_name')
reaction_equation = dmodels.TextField()
lb = dmodels.FloatField(null=True, blank=True)
ub = dmodels.FloatField(null=True, blank=True)
brenda = dmodels.CharField(max_length=13, blank=True)
kegg = dmodels.CharField(max_length=10, blank=True, di_show=True)
metacyc = dmodels.CharField(max_length=100, blank=True)
pubmed = dmodels.CharField(max_length=12, blank=True)
notes = dmodels.TextField(blank=True)
metabolite = dmodels.ManyToManyField(
'Metabolite',
related_name='reactions') #, through='ReactionMetabolite')
def __str__(self):
"""Return equation and database ID if exists in specified order."""
allowed_length = 30
if self.brenda:
return self.brenda
elif self.metacyc:
return self.metacyc
elif self.kegg:
return self.kegg
else:
if len(self.reaction_equation) < allowed_length:
return self.reaction_equation
else:
return self.reaction_equation[:30] + '[...]'
@property
def brendalink(self):
if self.brenda:
prefix = self.brenda[:2]
refid = self.brenda[2:]
link = '<a href="http://www.brenda-enzymes.org/structure.php?show=reaction&id={}&type={}&displayType=marvin">{}</a>'
if prefix == 'BS':
return format_html(link, mark_safe(refid), mark_safe('S'),
self.brenda)
elif prefix == 'BR':
return format_html(link, mark_safe(refid), mark_safe('I'),
self.brenda)
else:
return None
@property
def kegglink(self):
if self.kegg:
link = '<a href="http://www.genome.jp/dbget-bin/www_bget?rn:{}">{}</a>'
return format_html(link, mark_safe(self.kegg), self.kegg)
else:
return None
@property
def metacyclink(self):
if self.metacyc:
link = '<a href="http://metacyc.org/META/NEW-IMAGE?type=NIL&object={}&redirect=T">{}</a>'
return format_html(link, mark_safe(self.metacyc), self.metacyc)
else:
return None
@property
def db_crossref(self):
return (self.brendalink or self.kegglink or self.metacyclink
or 'No cross reference found.')
@property
def short_reaction(self):
allowed_length = 30
if len(self.reaction_id < allowed_length):
return self.reaction_id
else:
return self.reaction_id[:30] + '[...]'
class RNAseqData(TranscriptomeData):
mean_rpkm = dmodels.FloatField(di_show=True)
class Meta:
verbose_name_plural = 'RNASeq data'
class ExperimentalData(MeasurementModel):
mean = dmodels.FloatField(di_show=True)
class Meta:
abstract = True