def test_added_features():
genotype = Genotype.parse('+geneA -geneB +geneB -geneC')
assert genotype.added_features == {Feature('geneA')}
genotype = Genotype.parse('+{geneA, geneB:geneC}')
assert genotype.added_features == {
Feature('geneA'), Feature('geneB'),
Feature('geneC')
}
def test_genotype_gnomic_format(gnomic_formatter):
assert gnomic_formatter.format_genotype(Genotype.parse('+geneA -geneB site>feature')) \
== '+geneA -geneB site>feature'
assert gnomic_formatter.format_genotype(Genotype.parse('+geneA -geneB site>>feature')) \
== '+geneA -geneB site>feature'
assert gnomic_formatter.format_genotype(Genotype.parse('+geneA -geneB -geneA')) == '-geneB'
assert gnomic_formatter.format_genotype(Genotype.parse('+{geneA, geneB} -{geneC, geneD}')) \
== '+{geneA, geneB} -{geneC, geneD}'
def test_genotype_gnomic_format(gnomic_formatter):
assert gnomic_formatter.format_genotype(Genotype.parse('+geneA -geneB site>feature')) \
== '+geneA -geneB site>feature'
assert gnomic_formatter.format_genotype(Genotype.parse('+geneA -geneB site>>feature')) \
== '+geneA -geneB site>feature'
assert gnomic_formatter.format_genotype(
Genotype.parse('+geneA -geneB -geneA')) == '-geneB'
assert gnomic_formatter.format_genotype(Genotype.parse('+{geneA, geneB} -{geneC, geneD}')) \
== '+{geneA, geneB} -{geneC, geneD}'
def test_genotype_text_format(text_formatter):
assert text_formatter.format_genotype(Genotype.parse('+geneA')) == 'geneA'
assert text_formatter.format_genotype(Genotype.parse('-geneA')) == '\u0394geneA'
assert text_formatter.format_genotype(Genotype.parse('siteA>(pA)')) == '\u0394siteA\u2192(pA)'
assert text_formatter.format_genotype(Genotype.parse('foo>bar')) == '\u0394foo\u2192bar'
assert text_formatter.format_genotype(Genotype.parse('foo>>bar')) == '\u0394foo\u2192bar'
assert text_formatter.format_genotype(Genotype.parse('-(pA)')) == '\u0394(pA)'
assert text_formatter.format_genotype(Genotype.parse('+geneA(x)')) == 'geneA(x)'
assert text_formatter.format_genotype(Genotype.parse('+geneA(var1, var2)')) == 'geneA(var1; var2)'
assert text_formatter.format_genotype(Genotype.parse('+{geneA, geneB}')) == '{geneA, geneB}'
def to_gnomic(self):
if _gnomic_available_:
return Genotype([target.to_gnomic() for target in self.targets])
else:
raise SystemError(
"Gnomic is only compatible with python >= 3 (%i.%i)" %
(sys.version_info.major, sys.version_info.minor))
def test_added_fusion_features():
genotype = Genotype.parse(
'+geneA -geneB:geneC +geneB:geneC +{geneA, geneB}')
assert genotype.added_fusion_features == {
Feature('geneA'),
CompositeAnnotation(Feature('geneA'), Feature('geneB'))
}
def test_gnomic_integration_FluxModulationTarget(self, model):
# with pytest.raises(ValueError):
# FluxModulationTarget("test", 0, 0) # TODO: this should really not be possible
flux_modulation_target = FluxModulationTarget("test", 1, 0)
flux_modulation_target_gnomic = flux_modulation_target.to_gnomic()
assert genotype_to_string(Genotype([flux_modulation_target_gnomic
])) == "+flux.test(value=1)"
flux_modulation_target = FluxModulationTarget("PGK",
0.5,
1,
accession_id="PGK",
accession_db="bigg")
flux_modulation_target_gnomic = flux_modulation_target.to_gnomic()
assert genotype_to_string(Genotype([
flux_modulation_target_gnomic
])) == "+flux.PGK(value=0.5)#bigg:PGK"
def test_gnomic_integration_ReactionKnockinTarget(self, model):
reaction = Reaction(id="atpzase", name="Cosmic ATP generator")
atp_z = Metabolite(id="atp_z", name="Cosmic ATP", compartment="c")
reaction.add_metabolites({model.metabolites.atp_c: 1, atp_z: -1})
knockin_target = ReactionKnockinTarget("atpzase", reaction)
knockin_target_gnomic = knockin_target.to_gnomic()
assert genotype_to_string(Genotype([knockin_target_gnomic
])) == "+reaction.atpzase"
reaction.add_metabolites({model.metabolites.atp_c: 1, atp_z: -1})
knockin_target = ReactionKnockinTarget("atpzase",
reaction,
accession_id='atpzase',
accession_db='unicorn')
knockin_target_gnomic = knockin_target.to_gnomic()
assert genotype_to_string(Genotype(
[knockin_target_gnomic])) == "+reaction.atpzase#unicorn:atpzase"
def test_genotype_text_format(text_formatter):
assert text_formatter.format_genotype(Genotype.parse('+geneA')) == 'geneA'
assert text_formatter.format_genotype(
Genotype.parse('-geneA')) == '\u0394geneA'
assert text_formatter.format_genotype(
Genotype.parse('siteA>(pA)')) == '\u0394siteA\u2192(pA)'
assert text_formatter.format_genotype(
Genotype.parse('foo>bar')) == '\u0394foo\u2192bar'
assert text_formatter.format_genotype(
Genotype.parse('foo>>bar')) == '\u0394foo\u2192bar'
assert text_formatter.format_genotype(
Genotype.parse('-(pA)')) == '\u0394(pA)'
assert text_formatter.format_genotype(
Genotype.parse('+geneA(x)')) == 'geneA(x)'
assert text_formatter.format_genotype(
Genotype.parse('+geneA(var1, var2)')) == 'geneA(var1; var2)'
assert text_formatter.format_genotype(
Genotype.parse('+{geneA, geneB}')) == '{geneA, geneB}'
def test_gnomic_integration_ReactionCofactorSwapTarget(self, model):
cofactor_id_swaps = [("nad_c", "nadh_c"), ("nadp_c", "nadph_c")]
swap_pairs = ([
model.metabolites.get_by_id(m) for m in cofactor_id_swaps[0]
], [model.metabolites.get_by_id(m) for m in cofactor_id_swaps[1]])
swap_target = ReactionCofactorSwapTarget("GAPD", swap_pairs)
swap_target_gnomic = swap_target.to_gnomic()
assert genotype_to_string(Genotype([
swap_target_gnomic
])) == "+reaction.GAPD(nad_c=nadp_c;nadh_c=nadph_c)"
def test_gene_knockout_target(self, model):
gene = "b4025"
knockout_target = GeneKnockoutTarget(gene,
accession_id=gene,
accession_db='bigg')
knockout_target_gnomic = knockout_target.to_gnomic()
assert genotype_to_string(Genotype([knockout_target_gnomic
])) == "-b4025#bigg:b4025"
with model:
knockout_target.apply(model)
assert model.reactions.PGI.lower_bound == 0
assert model.reactions.PGI.upper_bound == 0
assert abs(model.optimize().f - 0.8631) < 0.0001
assert model.reactions.PGI.lower_bound == -1000
assert model.reactions.PGI.upper_bound == 1000
def test_genotype_html_format(html_formatter):
assert html_formatter.format_genotype(Genotype.parse('+geneA')) == '<span class="gnomic-feature">geneA</span>'
assert html_formatter.format_genotype(Genotype.parse('-geneB')) \
== '\u0394<span class="gnomic-feature">geneB</span>'
assert html_formatter.format_genotype(Genotype.parse('foo>>bar')) \
== '\u0394<span class="gnomic-feature">foo</span>\u2192<span class="gnomic-feature">bar</span>'
assert html_formatter.format_genotype(Genotype.parse('(pA)')) \
== '<span class="gnomic-plasmid">(<span class="gnomic-plasmid-name">pA</span>)</span>'
assert html_formatter.format_genotype(Genotype.parse('+geneA(x)')) \
== '<span class="gnomic-feature">geneA<sup>x</sup></span>'
assert html_formatter.format_genotype(Genotype.parse('+geneA(x; wild-type; mutant; y)')) \
== '<span class="gnomic-feature">geneA<sup>x; wild-type; mutant; y</sup></span>'
assert html_formatter.format_genotype(Genotype.parse('+foo:bar')) \
== '<span class="gnomic-fusion"><span class="gnomic-feature">foo</span>:' \
'<span class="gnomic-feature">bar</span></span>'
def test_genotype_html_format(html_formatter):
assert html_formatter.format_genotype(Genotype.parse(
'+geneA')) == '<span class="gnomic-feature">geneA</span>'
assert html_formatter.format_genotype(Genotype.parse('-geneB')) \
== '\u0394<span class="gnomic-feature">geneB</span>'
assert html_formatter.format_genotype(Genotype.parse('foo>>bar')) \
== '\u0394<span class="gnomic-feature">foo</span>\u2192<span class="gnomic-feature">bar</span>'
assert html_formatter.format_genotype(Genotype.parse('(pA)')) \
== '<span class="gnomic-plasmid">(<span class="gnomic-plasmid-name">pA</span>)</span>'
assert html_formatter.format_genotype(Genotype.parse('+geneA(x)')) \
== '<span class="gnomic-feature">geneA<sup>x</sup></span>'
assert html_formatter.format_genotype(Genotype.parse('+geneA(x; wild-type; mutant; y)')) \
== '<span class="gnomic-feature">geneA<sup>x; wild-type; mutant; y</sup></span>'
assert html_formatter.format_genotype(Genotype.parse('+foo:bar')) \
== '<span class="gnomic-fusion"><span class="gnomic-feature">foo</span>:' \
'<span class="gnomic-feature">bar</span></span>'
def test_at_locus_gnomic_format(gnomic_formatter):
assert gnomic_formatter.format_at_locus(AtLocus(Feature('foo'), Feature('bar'))) == 'foo@bar'
assert gnomic_formatter.format_genotype(Genotype.parse('foo@bar>new')) == 'foo@bar>new'
def test_at_locus_gnomic_format(gnomic_formatter):
assert gnomic_formatter.format_at_locus(
AtLocus(Feature('foo'), Feature('bar'))) == 'foo@bar'
assert gnomic_formatter.format_genotype(
Genotype.parse('foo@bar>new')) == 'foo@bar>new'
def _repr_html_(self):
return genotype_to_text(Genotype([self.to_gnomic()]))
def test_removed_fusions():
genotype = Genotype.parse('+A:B +B:C -B:C -C:D')
assert genotype.removed_fusions == {Fusion(Feature('C'), Feature('D'))}
def to_gnomic(self):
return Genotype([target.to_gnomic() for target in self.targets])
def test_added_plasmids():
genotype = Genotype.parse('+gene.B (pA) (pB) -(pB) -(pC)')
assert genotype.added_plasmids == {Plasmid('pA')}
def test_removed_features():
genotype = Genotype.parse('+geneA -geneB +geneB -geneC')
assert genotype.removed_features == {Feature('geneC')}
def __str__(self):
return genotype_to_string(Genotype([self.to_gnomic()]))
def test_removed_fusion_features():
genotype = Genotype.parse('+geneA -geneB:geneC -geneA +{geneA, geneB}')
assert genotype.removed_fusion_features == {
Fusion(Feature('geneB'), Feature('geneC'))
}
def test_added_fusions():
genotype = Genotype.parse('+A:B +B:C -B:C -C:D')
assert genotype.added_fusions == {Fusion(Feature('A'), Feature('B'))}
def parse(string):
return Genotype._parse_string(string,
organisms=DEFAULT_ORGANISMS,
types=DEFAULT_TYPES)
def test_removed_plasmids():
genotype = Genotype.parse('+gene.A (pA) (pB) -(pB) -(pC)')
assert genotype.removed_plasmids == {Plasmid('pC')}
def chain(*gnomic_strings, **kwargs):
parent = kwargs.pop('parent', None)
genotype = Genotype.parse(gnomic_strings[0], parent=parent, **kwargs)
for gnomic_string in gnomic_strings[1:]:
genotype = Genotype.parse(gnomic_string, parent=genotype, **kwargs)
return genotype
def chain(self, *definitions, **kwargs):
genotype = Genotype.parse(definitions[0], **kwargs)
for definition in definitions[1:]:
genotype = Genotype.parse(definition, parent=genotype, **kwargs)
return genotype
