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)
#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()
