示例#1
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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
示例#2
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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
示例#3
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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])
示例#4
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           '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)
示例#5
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    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])