Audit Codes

The Codes library provides a bunch of static data used in various analysis steps across the project. This page provides the unit tests, or audits, for that library.

Audit: Ascii To Bit Codes

TACG and tacg are encoded in the downloaded genome. The 4 ascii codes used in that file are displayed here. This audit requires checking against a published ascii/unicode table.

Note: 7 bit ascii is a subset of unicode. All downloaded genome data is 7 bit ascii.

The Bit Code shows the base2 decision tree pattern. Only 2 right bits matter, but if 1 in left position then an error

Bit Codes
Code Ascii Bit Code
T 84 000
t 116 000
A 65 011
a 97 011
C 67 010
c 99 010
G 71 001
g 103 001

Paleo Letter Encoding

This test demonstrates control over the various ways paleo is encoded and converted.

Sequence Letter Name Keys Punct?
0 Dot SPACE true
1 Wa a false
2 Ba b false
3 Ge g false
4 Du d false
5 Fe f false
6 Ve v false
7 Jo j i false
8 Ha h false
9 The x false
10 Yo y false
11 Ku k false
12 Lu l false
13 Mo m false
14 Ne n false
15 Sa s false
16 Oo o false
17 Pe p false
18 Ze z false
19 Qu q false
20 Re r false
21 The w false
22 Ta t false
23 Colon . true
24 Quad > true

Audit Codon Data

This audit displays all data that maps directly to codon data.

# is the input codon id. All other values derived from here.

Base2 is # expressed in base 2.

Codon is the 3 letter codon code for this base.

Dir indicates the Boustrophedon direction for this base. Should split the table in half top to bottom.

Id is the id computed from the Codon. Should match #.

pId is the paleo Id from this codon.

Paleo is the paleo Letter from this codon. Should match 3D models.

QO is quad ordinality, used to distinguish Paleo Quad letters.

# Base2 Codon Dir Id pId Paleo
0 000000 TTT R 0 0
1 000001 TTG R 1 23
2 000010 TTC R 2 6
3 000011 TTA R 3 17
4 000100 GTT R 4 12
5 000101 GTG R 5 11
6 000110 GTC R 6 1
7 000111 GTA R 7 22
8 001000 CTT R 8 14
9 001001 CTG R 9 9
10 001010 CTC R 10 20
11 001011 CTA R 11 3
12 001100 ATT R 12 8
13 001101 ATG R 13 15
14 001110 ATC R 14 19
15 001111 ATA R 15 4
16 010000 TGT R 16 10
17 010001 TGG R 17 13
18 010010 TGC R 18 21
19 010011 TGA R 19 2
20 010100 GGT R 20 16
21 010101 GGG R 21 7
22 010110 GGC R 22 5
23 010111 GGA R 23 18
24 011000 CGT R 24 24
25 011001 CGG R 25 25 1
26 011010 CGC R 26 26 2
27 011011 CGA R 27 27 3
28 011100 AGT R 28 28 4
29 011101 AGG R 29 29 5
30 011110 AGC R 30 30 6
31 011111 AGA R 31 31 7
32 100000 TCT L 32 31 7
33 100001 TCG L 33 30 6
34 100010 TCC L 34 29 5
35 100011 TCA L 35 28 4
36 100100 GCT L 36 27 3
37 100101 GCG L 37 26 2
38 100110 GCC L 38 25 1
39 100111 GCA L 39 24
40 101000 CCT L 40 5
41 101001 CCG L 41 18
42 101010 CCC L 42 7
43 101011 CCA L 43 16
44 101100 ACT L 44 2
45 101101 ACG L 45 21
46 101110 ACC L 46 13
47 101111 ACA L 47 10
48 110000 TAT L 48 4
49 110001 TAG L 49 19
50 110010 TAC L 50 15
51 110011 TAA L 51 8
52 110100 GAT L 52 3
53 110101 GAG L 53 20
54 110110 GAC L 54 9
55 110111 GAA L 55 14
56 111000 CAT L 56 22
57 111001 CAG L 57 1
58 111010 CAC L 58 11
59 111011 CAA L 59 12
60 111100 AAT L 60 6
61 111101 AAG L 61 17
62 111110 AAC L 62 23
63 111111 AAA L 63 0

Codon Buffer Audit

Many code steps involve buffers with either codon or paleo data. The following table shows conversions between these structures.

# is the index into a 63 entry buffer. This buffer is initialized to a codon code of # itself.

Codon is the normal codon for this entry.

C-base2 is the base 2 number for this codon.

Paleo is the paleo conversion for this codon.

P-base2 is the paleo letter number in base 2.

Codon Codes Buffer Audit
# Codon C-base2 Paleo P-base2 Punct?
0 TTT 00000000 01000000 true
1 TTG 00000001 01010111 true
2 TTC 00000010 00000110 false
3 TTA 00000011 00010001 false
4 GTT 00000100 00001100 false
5 GTG 00000101 00001011 false
6 GTC 00000110 00000001 false
7 GTA 00000111 00010110 false
8 CTT 00001000 00001110 false
9 CTG 00001001 00001001 false
10 CTC 00001010 00010100 false
11 CTA 00001011 00000011 false
12 ATT 00001100 00001000 false
13 ATG 00001101 00001111 false
14 ATC 00001110 00010011 false
15 ATA 00001111 00000100 false
16 TGT 00010000 00001010 false
17 TGG 00010001 00001101 false
18 TGC 00010010 00010101 false
19 TGA 00010011 00000010 false
20 GGT 00010100 00010000 false
21 GGG 00010101 00000111 false
22 GGC 00010110 00000101 false
23 GGA 00010111 00010010 false
24 CGT 00011000 01011000 true
25 CGG 00011001 1 01011001 true
26 CGC 00011010 2 01011010 true
27 CGA 00011011 3 01011011 true
28 AGT 00011100 4 01011100 true
29 AGG 00011101 5 01011101 true
30 AGC 00011110 6 01011110 true
31 AGA 00011111 7 01011111 true
32 TCT 00100000 7 01011111 true
33 TCG 00100001 6 01011110 true
34 TCC 00100010 5 01011101 true
35 TCA 00100011 4 01011100 true
36 GCT 00100100 3 01011011 true
37 GCG 00100101 2 01011010 true
38 GCC 00100110 1 01011001 true
39 GCA 00100111 01011000 true
40 CCT 00101000 00000101 false
41 CCG 00101001 00010010 false
42 CCC 00101010 00000111 false
43 CCA 00101011 00010000 false
44 ACT 00101100 00000010 false
45 ACG 00101101 00010101 false
46 ACC 00101110 00001101 false
47 ACA 00101111 00001010 false
48 TAT 00110000 00000100 false
49 TAG 00110001 00010011 false
50 TAC 00110010 00001111 false
51 TAA 00110011 00001000 false
52 GAT 00110100 00000011 false
53 GAG 00110101 00010100 false
54 GAC 00110110 00001001 false
55 GAA 00110111 00001110 false
56 CAT 00111000 00010110 false
57 CAG 00111001 00000001 false
58 CAC 00111010 00001011 false
59 CAA 00111011 00001100 false
60 AAT 00111100 00000110 false
61 AAG 00111101 00010001 false
62 AAC 00111110 01010111 true
63 TTT 00000000 01000000 true
Phil Stone 2022-08-28