def return_equal_charge_concentrations(protein_file,
                                       RNA_file,
                                       protein_conc=1000,
                                       count_histidine=0,
                                       count_gfp=1):

    protein = list(SeqIO.parse(protein_file, 'fasta'))
    RNAS = list(SeqIO.parse(RNA_file, 'fasta'))

    pos_protein = 0
    for p in protein:
        protein_obj = SequenceParameters(str(p.seq))
        pos_protein = protein_obj.get_countPos() - protein_obj.get_countNeg()

    GFP = SequenceParameters(
        "MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK"
    )

    if count_histidine:
        pos_protein = pos_protein + 0.5 * protein_obj.get_amino_acid_fractions(
        )['H'] * (protein_obj.get_length())
    if count_gfp:
        pos_protein = pos_protein + (GFP.get_countPos() - GFP.get_countNeg())
    counter_conc_max = {}
    for rna in RNAS:
        counter_conc_max[rna.id.split('(')
                         [0]] = protein_conc * pos_protein / len(rna.seq)

    return (counter_conc_max)
Ejemplo n.º 2
0
    #can't use SeqParam(seqfile=file)
    #because all the sequences are appended to each other.
    output = open(file + "_charge", 'w+')
    for protein in [x for x in contents if x]:

        header = protein[0:protein.index('\n')]
        seq = protein[protein.index('\n'):-1]

        print(header)
        if ('X' in seq):
            print("Warning: unspecified protein encountered.")
        seq = seq.replace('X', '')

        seq_param = SequenceParameters(seq)

        #mean_net_charge is always positive, whereas
        # net_charge_per_residue is alternating
        net_charge = seq_param.get_NCPR(pH=7.0) * seq_param.get_length()
        print(net_charge)

        output.write(header)
        output.write(", ")
        output.write(str(7.0))
        output.write(str(", "))
        output.write(str(seq_param.get_molecular_weight()))
        output.write(str(", "))
        output.write(str(net_charge))
        output.write('\n')

    output.close()