def build_transcriptome(transcriptome_size, gene_library):
print "building transcriptome..."
#print len(gene_library)
transcribed_genes = [random.choice(gene_library.items()) for n in range(transcriptome_size)]
transcribed_genes = [(name, sequence.lower().replace('t', 'u')) for name, sequence in transcribed_genes]
mRNAs = [MRNA_specific.mRNA_spec(index=n, sequence=transcribed_genes[n][1], geneID=transcribed_genes[n][0]) for n in range(transcriptome_size)]
pickle.dump(mRNAs, open(os.path.join("mRNA_"+str(transcriptome_size)+".pkl"), "wb"))
return mRNAs
def build_transcriptome(transcriptome_size, gene_library):
print "building transcriptome..."
#print len(gene_library)
transcribed_genes = [
random.choice(gene_library.items()) for n in range(transcriptome_size)
]
transcribed_genes = [(name, sequence.lower().replace('t', 'u'))
for name, sequence in transcribed_genes]
mRNAs = [
MRNA_specific.mRNA_spec(index=n,
sequence=transcribed_genes[n][1],
geneID=transcribed_genes[n][0])
for n in range(transcriptome_size)
]
pickle.dump(
mRNAs,
open(os.path.join("mRNA_" + str(transcriptome_size) + ".pkl"), "wb"))
return mRNAs
peptide_bonds, proteins = [], []
for duration in durations:
print "#############################################################################################################"
print "duration =", duration
print "#############################################################################################################"
for k, alpha in enumerate(alphas):
print "#############################################################################################################"
print "alpha =", alpha
print "#############################################################################################################"
# 1 mRNA
mRNAs = [
MRNA_specific.mRNA_spec(index=0,
sequence=examplesequence,
geneID=1)
]
gene_library = {1: examplesequence}
tr = TRSL_specific.TRSL_spec(mRNAs, gene_library)
tr.tRNA = col.Counter({
i: int(TRSL_specific.tRNA_types[i]['abundancy'] *
attenuation_factors[i][k])
for i in TRSL_specific.tRNA_types
})
#tr.tRNA = col.Counter({i:TRSL_specific.tRNA_types[i]['abundancy'] for i in TRSL_specific.tRNA_types})
#tr.tRNA[13] = 0 # we modify a relevant tRNA
tr.tRNA_free = col.Counter({
i: int(TRSL_specific.tRNA_types[i]['abundancy'] *
attenuation_factors[i][k])
'exome': pkl.load(open("../parameters/orf_coding.p", "rb")),
'transcriptome': pkl.load(open("../parameters/transcriptome_plotkin.p", "rb")),
'init_rates': pkl.load(open("../parameters/init_rates_plotkin.p", "rb")),
'decay_constants': pkl.load(open("../parameters/decay_constants.p", "rb")),
'description': 'full transcriptome and exome, with decay, specific best estimate initiation rates according to Plotkin'
}
genes = list(set(conf['exome']) & set(conf['transcriptome']) & set(conf['init_rates']) & set(conf['decay_constants']))
print "found %s genes in common." % len(genes)
mRNAs = []
counter = 0
for gene in genes:
# print "abundancies and initiation rates available for gene:", gene
for instance in range(conf['transcriptome'][gene]):
mRNAs.append(MRNA_specific.mRNA_spec(index=counter, sequence=conf['exome'][gene], geneID=gene, ribosomes={}, init_rate=conf['init_rates'][gene])) # do not just multiply the list
counter += 1
print "built gene library, next: run TRSL_spec."
description = conf['description']
print description
duration = 20.0
tr = TRSL_spec(mRNAs, conf['exome'], conf['decay_constants'], nribo=20000)
tr._tRNA = col.Counter({i: tRNA_types[i]['abundancy'] for i in tRNA_types})
tr._tRNA_free = col.Counter({i: int(tr._tRNA[i]) for i in tRNA_types}) # tRNA not bound to ribosomes
tr._tRNA_bound = tr._tRNA - tr._tRNA_free # tRNA bound to ribosomes
tr.solve_internal(0.0, duration, deltat=1.0)
genes = list(
set(conf['exome']) & set(conf['transcriptome'])
& set(conf['init_rates']) & set(conf['decay_constants']))
print "found %s genes in common." % len(genes)
mRNAs = []
counter = 0
for gene in genes:
# print "abundancies and initiation rates available for gene:", gene
for instance in range(conf['transcriptome'][gene]):
mRNAs.append(
MRNA_specific.mRNA_spec(
index=counter,
sequence=conf['exome'][gene],
geneID=gene,
ribosomes={},
init_rate=conf['init_rates']
[gene])) # do not just multiply the list
counter += 1
print "built gene library, next: run TRSL_spec."
description = conf['description']
print description
duration = 20.0
tr = TRSL_spec(mRNAs, conf['exome'], conf['decay_constants'], nribo=20000)
tr._tRNA = col.Counter({i: tRNA_types[i]['abundancy'] for i in tRNA_types})
tr._tRNA_free = col.Counter({i: int(tr._tRNA[i])