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3.3 years ago
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those are the data
Phe UUU 1483 1.14 Ser UCU 1094 1.47 Tyr UAU 1000 1.12 Cys UGU 434 1.18
UUC 1117 0.86 UCC 773 1.04 UAC 789 0.88 UGC 303 0.82
Leu UUA 1349 1.55 UCA 882 1.19 TER UAA 47 1.27 TER UGA 36 0.97
UUG 1549 1.78 UCG 487 0.66 UAG 28 0.76 Trp UGG 665 1.00
CUU 698 0.80 Pro CCU 747 1.27 His CAU 677 1.15 Arg CGU 328 0.86
CUC 364 0.42 CCC 415 0.71 CAC 499 0.85 CGC 171 0.45
CUA 671 0.77 CCA 911 1.55 Gln CAA 1388 1.35 CGA 151 0.39
CUG 604 0.69 CCG 281 0.48 CAG 668 0.65 CGG 103 0.27
Ile AUU 1612 1.35 Thr ACU 1052 1.38 Asn AAU 1778 1.17 Ser AGU 717 0.97
AUC 1018 0.85 ACC 660 0.87 AAC 1262 0.83 AGC 500 0.67
AUA 943 0.79 ACA 883 1.16 Lys AAA 2118 1.13 Arg AGA 1038 2.71
Met AUG 1156 1.00 ACG 444 0.58 AAG 1645 0.87 AGG 504 1.32
Val GUU 1184 1.49 Ala GCU 1055 1.40 Asp GAU 1905 1.25 Gly GGU 1284 1.87
GUC 674 0.85 GCC 765 1.01 GAC 1145 0.75 GGC 552 0.80
GUA 622 0.78 GCA 836 1.11 Glu GAA 2371 1.41 GGA 557 0.81
GUG 690 0.87 GCG 368 0.49 GAG 995 0.59 GGG 355 0.52
53400 codons (used Universal Genetic code)
How do I calculate the relative frequency of each codon and generate a new table?
I have a database with tables like this and I would like to calculate the relative frequency as follows:
1483 (codon value) / 53400 (total codon value) = 0.02777153558 (relative frequency)
I tried to do it that way and was unsuccessful
code:
import pymysql as MySQLdb
conexao = MySQLdb.connect(
host = "localhost",
user = "xxx",
passwd = "xxx",
db = "name_table"
)
banco = conexao.cursor()
#Frequency relative
banco.execute(
select * from name_table;
set @total = (select total from name_table);
set @ni = (select AAA, BBB from name_table)
@ni/@total
)
banco.fetchall()
for i in banco.fetchall():
print(i)
conexao.close()