class GeneLocus(core.PolymerLocus):
""" Knowledge of a gene
Attributes:
symbol (:obj:`str`): symbol
Related attributes:
proteins (:obj:`list` of :obj:`ProteinSpeciesType`): protein
"""
symbol = obj_tables.StringAttribute()
start = obj_tables.IntegerAttribute()
end = obj_tables.IntegerAttribute()
is_essential = obj_tables.BooleanAttribute()
proteins = obj_tables.OneToOneAttribute(ProteinSpeciesType,
related_name='gene')
homologs = obj_tables.LongStringAttribute()
evidence = obj_tables.OneToManyAttribute(core.Evidence,
related_name='genes')
cog = obj_tables.sci.onto.OntoTermAttribute(
kbOnt, terms=kbOnt['WC:COG'].subclasses(), none=True)
class Meta(obj_tables.Model.Meta):
verbose_name = 'Gene'
verbose_name_plural = 'Genes'
attribute_order = ('id', 'name', 'synonyms', 'symbol', 'polymer',
'start', 'end', 'cog', 'homologs', 'is_essential',
'proteins', 'evidence', 'identifiers', 'references',
'comments')
class SparseMatrixOrdered(obj_tables.Model):
row_number = obj_tables.IntegerAttribute(verbose_name='RowNumber')
column_number = obj_tables.IntegerAttribute(verbose_name='ColumnNumber')
value = obj_tables.FloatAttribute(verbose_name='Value')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'row_number',
'column_number',
'value',
)
verbose_name = 'SparseMatrixOrdered'
verbose_name_plural = 'SparseMatrixOrdered'
class rxnconContingencyList(obj_tables.Model):
u_i_d_contingency = obj_tables.IntegerAttribute(
verbose_name='UID:Contingency')
target = obj_tables.StringAttribute(verbose_name='Target')
contingency = obj_tables.StringAttribute(verbose_name='Contingency')
modifier = obj_tables.StringAttribute(verbose_name='Modifier')
reference_identifiers_pubmed = obj_tables.StringAttribute(
verbose_name='Reference:Identifiers:pubmed')
quality = obj_tables.StringAttribute(verbose_name='Quality')
comment = obj_tables.StringAttribute(verbose_name='Comment')
internal_complex_i_d = obj_tables.StringAttribute(
verbose_name='InternalComplexID')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'u_i_d_contingency',
'target',
'contingency',
'modifier',
'reference_identifiers_pubmed',
'quality',
'comment',
'internal_complex_i_d',
)
verbose_name = 'rxnconContingencyList'
verbose_name_plural = 'rxnconContingencyList'
class TranscriptionUnitLocus(core.PolymerLocus):
""" Knowledge about an open reading frame
Attributes:
genes (:obj:`list` of :obj:`GeneLocus`): genes
"""
pribnow_start = obj_tables.IntegerAttribute()
pribnow_end = obj_tables.IntegerAttribute()
genes = obj_tables.OneToManyAttribute('GeneLocus',
related_name='transcription_units')
rnas = obj_tables.ManyToManyAttribute('RnaSpeciesType',
related_name='transcription_units')
#type = obj_tables.sci.onto.OntoTermAttribute(kbOnt,
# terms = kbOnt['WC:gene'].subclasses(),
# none=True)
class Meta(obj_tables.Model.Meta):
verbose_name = 'Transcription unit'
verbose_name_plural = 'Transcription units'
attribute_order = ('id', 'name', 'polymer', 'strand', 'pribnow_start',
'pribnow_end', 'start', 'end', 'rnas', 'genes',
'identifiers', 'references', 'comments')
def get_3_prime(self):
""" Get the 3' coordinate
Returns:
:obj:`int`: 3' coordinate
"""
if self.get_direction() == core.PolymerDirection.forward:
return self.end
else:
return self.start
def get_5_prime(self):
""" Get the 5' coordinate
Returns:
:obj:`int`: 5' coordinate
"""
if self.get_direction() == core.PolymerDirection.forward:
return self.start
else:
return self.end
class rxnconReactionList(obj_tables.Model):
i_d = obj_tables.IntegerAttribute(verbose_name='ID')
u_i_d_reaction = obj_tables.StringAttribute(verbose_name='UID:Reaction')
component_a_name = obj_tables.StringAttribute(
verbose_name='ComponentA:Name')
component_a_domain = obj_tables.StringAttribute(
verbose_name='ComponentA:Domain')
component_a_residue = obj_tables.StringAttribute(
verbose_name='ComponentA:Residue')
reaction = obj_tables.StringAttribute(verbose_name='Reaction')
component_b_name = obj_tables.StringAttribute(
verbose_name='ComponentB:Name')
component_b_domain = obj_tables.StringAttribute(
verbose_name='ComponentB:Domain')
component_b_residue = obj_tables.StringAttribute(
verbose_name='ComponentB:Residue')
quality = obj_tables.StringAttribute(verbose_name='Quality')
literature_identifiers_pubmed = obj_tables.StringAttribute(
verbose_name='Literature:Identifiers:pubmed')
comment = obj_tables.StringAttribute(verbose_name='Comment')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'i_d',
'u_i_d_reaction',
'component_a_name',
'component_a_domain',
'component_a_residue',
'reaction',
'component_b_name',
'component_b_domain',
'component_b_residue',
'quality',
'literature_identifiers_pubmed',
'comment',
)
verbose_name = 'rxnconReactionList'
verbose_name_plural = 'rxnconReactionList'
class Relationship(obj_tables.Model):
i_d = obj_tables.StringAttribute(verbose_name='ID')
from_object = obj_tables.StringAttribute(verbose_name='FromObject')
to_object = obj_tables.StringAttribute(verbose_name='ToObject')
value = obj_tables.IntegerAttribute(verbose_name='Value')
is_symmetric = obj_tables.BooleanAttribute(verbose_name='IsSymmetric')
sign = obj_tables.EnumAttribute(['+', '-', '0'],
default='0',
verbose_name='Sign')
relation = obj_tables.StringAttribute(verbose_name='Relation')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'i_d',
'from_object',
'to_object',
'value',
'is_symmetric',
'sign',
'relation',
)
verbose_name = 'Relationship'
verbose_name_plural = 'Relationship'
class Compound(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(
verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(
verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
s_b_m_l_species_id = obj_tables.StringAttribute(
verbose_name='SBML:species:id')
s_b_m_l_speciestype_id = obj_tables.StringAttribute(
verbose_name='SBML:speciestype:id')
initial_value = obj_tables.FloatAttribute(verbose_name='InitialValue')
initial_concentration = obj_tables.FloatAttribute(
verbose_name='InitialConcentration')
unit = obj_tables.StringAttribute(verbose_name='Unit')
location = obj_tables.StringAttribute(verbose_name='Location')
state = obj_tables.StringAttribute(verbose_name='State')
compound_sum_formula = obj_tables.StringAttribute(
verbose_name='CompoundSumFormula')
structure_formula = obj_tables.StringAttribute(
verbose_name='StructureFormula')
charge = obj_tables.IntegerAttribute(verbose_name='Charge')
mass = obj_tables.FloatAttribute(verbose_name='Mass')
is_constant = obj_tables.BooleanAttribute(verbose_name='IsConstant')
enzyme_role = obj_tables.StringAttribute(verbose_name='EnzymeRole')
regulator_role = obj_tables.StringAttribute(verbose_name='RegulatorRole')
s_b_o_term = obj_tables.StringAttribute(verbose_name='SBOTerm')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
identifiers_sbo_kegg = obj_tables.StringAttribute(
verbose_name='Identifiers:sbo.kegg')
identifiers_kegg_compound = obj_tables.StringAttribute(
verbose_name='Identifiers:kegg.compound')
identifiers_obo_chebi = obj_tables.StringAttribute(
verbose_name='Identifiers:obo.chebi')
s_b_m_l_fbc_chemical_formula = obj_tables.StringAttribute(
verbose_name='SBML:fbc:ChemicalFormula')
s_b_m_l_fbc_charge = obj_tables.FloatAttribute(
verbose_name='SBML:fbc:Charge')
has_only_substance_units = obj_tables.BooleanAttribute(
verbose_name='HasOnlySubstanceUnits')
name_for_plots = obj_tables.StringAttribute(verbose_name='NameForPlots')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
's_b_m_l_species_id',
's_b_m_l_speciestype_id',
'initial_value',
'initial_concentration',
'unit',
'location',
'state',
'compound_sum_formula',
'structure_formula',
'charge',
'mass',
'is_constant',
'enzyme_role',
'regulator_role',
's_b_o_term',
'identifiers',
'identifiers_sbo_kegg',
'identifiers_kegg_compound',
'identifiers_obo_chebi',
's_b_m_l_fbc_chemical_formula',
's_b_m_l_fbc_charge',
'has_only_substance_units',
'name_for_plots',
)
verbose_name = 'Compound'
verbose_name_plural = 'Compound'
class RnaSpeciesType(core.PolymerSpeciesType):
""" Knowledge of an RNA species
Attributes:
transcription_units (:obj:`list` of :obj:`TranscriptionUnitLocus`): transcription units
type (:obj:`RnaType`): type
Related attributes:
proteins (:obj:`list` of :obj:`ProteinSpeciesType`): protein(s)
"""
start = obj_tables.IntegerAttribute()
end = obj_tables.IntegerAttribute()
proteins = obj_tables.OneToManyAttribute('ProteinSpeciesType',
related_name='rnas')
coordinate = obj_tables.IntegerAttribute()
length = obj_tables.IntegerAttribute()
type = obj_tables.sci.onto.OntoTermAttribute(
kbOnt, terms=kbOnt['WC:RNA'].subclasses(), none=True)
class Meta(obj_tables.Model.Meta):
verbose_name = 'RNA'
verbose_name_plural = 'RNAs'
attribute_order = ('id', 'name', 'synonyms', 'type', 'start', 'end',
'proteins', 'identifiers', 'references', 'comments')
def get_seq(self):
""" Get the sequence
Returns:
:obj:`Bio.Seq.Seq`: sequence
"""
tu = self.transcription_units[0]
tu_start = tu.start
tu_end = tu.end
dna_seq = tu.polymer.get_subseq(start=tu_start,
end=tu_end,
strand=tu.strand)
#tu_start = self.start
#dna_seq = self.transcription_units[0].polymer.get_subseq(start=tu_start, end=tu_end)
return dna_seq.transcribe()
def get_empirical_formula(self):
""" Get the empirical formula for an RNA transcript with
* 5' monophosphate
* Deprotonated phosphate oxygens
:math:`N_A * AMP + N_C * CMP + N_G * GMP + N_U * UMP - (L-1) * OH`
Returns:
:obj:`chem.EmpiricalFormula`: empirical formula
"""
seq = self.get_seq()
n_a = seq.upper().count('A')
n_c = seq.upper().count('C')
n_g = seq.upper().count('G')
n_u = seq.upper().count('U')
l = len(seq)
formula = chem.EmpiricalFormula()
formula.C = 10 * n_a + 9 * n_c + 10 * n_g + 9 * n_u
formula.H = 12 * n_a + 12 * n_c + 12 * n_g + 11 * n_u - (l - 1)
formula.N = 5 * n_a + 3 * n_c + 5 * n_g + 2 * n_u
formula.O = 7 * n_a + 8 * n_c + 8 * n_g + 9 * n_u - (l - 1)
formula.P = n_a + n_c + n_g + n_u
return formula
def get_charge(self):
""" Get the charge for a transcript with
* 5' monophosphate
* Deprotonated phosphate oxygens
:math:`-L - 1`
Returns:
:obj:`int`: charge
"""
return -self.get_len() - 1
def get_mol_wt(self):
""" Get the molecular weight for a transcript with
* 5' monophosphate
* Deprotonated phosphate oxygens
Returns:
:obj:`float`: molecular weight (Da)
"""
return self.get_empirical_formula().get_molecular_weight()
def get_direction(self):
""" Returns the direction of the polymer feature defind by its strand and start/end coordinate
Returns:
:obj:`str`: direction (in ['forward', 'reverse'])
Raises:
:obj:`ValueError`: start and end coordinate of chromosome feature can not be the same
:obj:`Exception`: strand is not member of PolymerStrand
"""
if self.start < self.end:
if self.strand == core.PolymerStrand.positive:
return core.PolymerDirection.forward
elif self.strand == core.PolymerStrand.negative:
return core.PolymerDirection.reverse
else:
raise Exception(
'Unrecognized polymer strand ({}) found for {}.'.format(
self.strand, self.id))
elif self.start > self.end:
if self.strand == core.PolymerStrand.positive:
return core.PolymerDirection.reverse
elif self.strand == core.PolymerStrand.negative:
return core.PolymerStrand.forward
else:
raise Exception(
'Unrecognized polymer strand ({}) found for {}.'.format(
self.strand, self.id))
elif self.start == self.end:
raise ValueError(
'Start and end position of chromosome feature can not be the same (Chrom feature id: {}).'
.format(self.id))