def test_termination_condition(self):
testMRNA = MRNA_specific.mRNA_spec(index=0,
sequence="agcaaguga",
geneID=None,
ribosomes={6: None},
init_rate=1e-3)
self.assertTrue(testMRNA.termination_condition())
# run simulation
# Einschwingvorgang: reichen 900 s?
burnin = 900
for start, stop, growth_factor in zip(switch_times[:-1], switch_times[1:], growth_factor_range):
print "simulating from {} to {}...".format(start, stop)
transcriptome = transcriptomes_dict[start/60]
mRNAs = []
counter = 0
#description = 'polyphasic cell cycle from {} to {}, updated Shah transcriptome, full exome, no decay, with ribo growth factor updated initiation rates according to Shah'.format(start, stop)
description = 'polyphasic cell cycle from {} to {}, updated Shah transcriptome, full exome, no decay, without ribo growth factor updated initiation rates according to Shah'.format(start, stop)
for gene in genes:
for transcript in range(transcriptome[gene]):
mRNAs.append(MRNA_specific.mRNA_spec(index=counter, sequence=exome[gene], geneID=gene, ribosomes={}, init_rate=init_rates[gene])) # do not just multiply the list
counter += 1
print "created transcriptome at time {}.".format(start)
tr = TRSL_specific.TRSL_spec(mRNAs, exome, decay_constants, int(nribo_start*growth_factor), proteome=col.Counter({}), detail=True)
# tr._tRNA = col.Counter({i: TRSL_specific.tRNA_types[i]['abundancy'] for i in TRSL_specific.tRNA_types})
tr._tRNA = col.Counter({i: int(TRSL_specific.tRNA_types[i]['abundancy'] * len(genes) / len(exome) * growth_factor) for i in TRSL_specific.tRNA_types})
tr._tRNA_free = col.Counter({i: int(tr._tRNA[i]) for i in TRSL_specific.tRNA_types}) # tRNA not bound to ribosomes
tr._tRNA_bound = tr._tRNA - tr._tRNA_free # tRNA bound to ribosomes
# Run without profiling:
tr.solve_internal(start, stop+burnin, deltat=1.0)
'''
# Run with profiling:
print(
"TRSL_dynamic_cell_cycle_volume_effects: simulating from {} to {}...".
format(start, stop))
transcriptome = transcriptomes_dict[start / 60]
mRNAs = []
counter = 0
description = 'volume-adjusted polyphasic cell cycle v2 from {} to {}, Teufel transcriptome, full exome, no decay, with ribo growth factor, updated initiation rates according to Shah'.format(
start, stop)
for gene in genes:
for transcript in range(transcriptome[gene]):
mRNAs.append(
MRNA_specific.mRNA_spec(index=counter,
sequence=exome[gene],
geneID=gene,
ribosomes={},
init_rate=init_rates[gene])
) # do not just multiply the list
counter += 1
print(
"TRSL_dynamic_cell_cycle_volume_effects: created transcriptome at time {}."
.format(start))
tr = TRSL_specific.TRSL_spec(mRNAs,
exome,
None,
int(nribo_start * growth_factor),
proteome=col.Counter({}),
detail=True)
genes = list(set(conf[i]['exome']) & set(conf[i]['transcriptome']) & set(conf[i]['init_rates']) & set(
conf[i]['decay_constants']))
else:
genes = list(set(conf[i]['exome']) & set(conf[i]['transcriptome']) & set(conf[i]['init_rates']))
conf[i]['decay_constants'] = None
print "found %s genes in common." % len(genes)
mRNAs = []
counter = 0
for gene in genes:
if conf[i]['init_rates']:
if gene in conf[i]['transcriptome'] and gene in conf[i]['init_rates']:
print "abundancies and initiation rates available for gene:", gene
for instance in range(conf[i]['transcriptome'][gene]):
mRNAs.append(MRNA_specific.mRNA_spec(index=counter,
sequence=conf[i]['exome'][gene],
geneID=gene,
ribosomes={},
init_rate=conf[i]['init_rates'][gene]))
counter += 1
else:
if gene in conf[i]['transcriptome']:
print "abundancies but no initiation rate available for gene:", gene
for instance in range(conf[i]['transcriptome'][gene]):
mRNAs.append(MRNA_specific.mRNA_spec(index=counter, sequence=conf[i]['exome'][gene], geneID=gene,
ribosomes={})) # do not just multiply the list
counter += 1
print "built gene library, next: run TRSL_spec."
description = conf[i]['description']
print description
duration = 1200.0 # should be sufficent to saturate
ribonumbers = range(50000, 550000, 50000)
for ribonumber in ribonumbers:
scaling_factor = ribonumber * 1.0 / 200000
for transcriptome_ID in transcriptomes_dict:
mRNAs = []
description = '{} ribosomes, {} phase transcriptome, varying tRNAs, full exome, no decay, median-enhanced initiation rates according to Shah'.format(ribonumber, transcriptome_ID)
counter = 0
genes = list(set(exome) & set(transcriptomes_dict[transcriptome_ID]) & set(init_rates))
print "found %s genes in common." % len(genes)
for gene in genes:
for transcript in range(transcriptomes_dict[transcriptome_ID][gene]):
mRNAs.append(MRNA_specific.mRNA_spec(index=counter, sequence=exome[gene], geneID=gene, ribosomes={}, init_rate=init_rates[gene])) # do not just multiply the list
counter += 1
print "created transcriptome: {}.".format(description)
tr = TRSL_specific.TRSL_spec(mRNAs, exome, decay_constants=None, nribo=ribonumber, proteome=col.Counter({}), detail=False)
# tr._tRNA = col.Counter({i: TRSL_specific.tRNA_types[i]['abundancy'] for i in TRSL_specific.tRNA_types})
tr._tRNA = col.Counter({i: int(TRSL_specific.tRNA_types[i]['abundancy'] * scaling_factor * len(genes) / len(exome)) for i in TRSL_specific.tRNA_types}) # this time we do let tRNA vary like the ribosomes
tr._tRNA_free = col.Counter({i: int(tr._tRNA[i]) for i in TRSL_specific.tRNA_types}) # tRNA not bound to ribosomes
tr._tRNA_bound = tr._tRNA - tr._tRNA_free # tRNA bound to ribosomes
# Run without profiling:
# tr.solve_internal(0, duration, deltat=0.2)
# Run with profiling:
set(conf[i]['exome']) & set(conf[i]['transcriptome'])
& set(conf[i]['init_rates']))
conf[i]['decay_constants'] = None
print "found %s genes in common." % len(genes)
mRNAs = []
counter = 0
for gene in genes:
if conf[i]['init_rates']:
if gene in conf[i]['transcriptome'] and gene in conf[i][
'init_rates']:
print "abundancies and initiation rates available for gene:", gene
for instance in range(conf[i]['transcriptome'][gene]):
mRNAs.append(
MRNA_specific.mRNA_spec(
index=counter,
sequence=conf[i]['exome'][gene],
geneID=gene,
ribosomes={},
init_rate=conf[i]['init_rates'][gene]))
counter += 1
else:
if gene in conf[i]['transcriptome']:
print "abundancies but no initiation rate available for gene:", gene
for instance in range(conf[i]['transcriptome'][gene]):
mRNAs.append(
MRNA_specific.mRNA_spec(
index=counter,
sequence=conf[i]['exome'][gene],
geneID=gene,
ribosomes={})) # do not just multiply the list
counter += 1
print "built gene library, next: run TRSL_spec."
