Thursday, September 24, 2015

Basic Fractal

Fractal: Recursiveness taken to a certain limit

This is an elementary fractal: In a given coordinates center n lines then in each center of those lines repeat the process.

Once the idea is clear then the interesting part is CODING which is not always easy. You got to have clear concept of recursiveness.

See the original post in this thread back in Fri Jul 03, 09 09:27 AM - I just added some color.

Tuesday, September 22, 2015

Chaos Game

Wednesday, August 26, 2015

Algorithms for DNA Sequencing 002

COURSERA Python for Genomic Data Science > Final Exam

°ExSan++ High Perfomance C++ Computing V.6.00.A°

Wed Aug 26 08:25:21 2015

exsan.plusplus@gmail.com https://twitter.com/#!/ExSan_com

JOB: gen_hw1_2521

Data File: c:\exsan\exsan_data\dna.example.txt

Basis Counter: 55782

ExSan Pages: 35

Total Basis counter = 55783

n_A = 9957 n_C = 17966 n_G = 18126 n_T = 9734 n_N = 0 total: 55783 ***n_GC = 36092

% A: 17.8495 C: 32.2069 G: 32.4938 T: 17.4498 N: 0

check-sum-> 1

Basis First Page

WORKSHEET A[40, 40] CHAR

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z AA AB AC AD AE AF AG AH AI AJ AK AL AM AN

>------------------------------------------------------------------------------------------------------------------------<

1: T C G G G C G A A G G C G G C A G C A A G T C G T C C A C G C G C A G C G C G G

2: C A C C G C G G G C C T C T G C C G T G C G C T G C T T G G C C A T G G C C T C

3: C A G C G C A C C G A T C G G A T C A A A G C C G C T G A A G C C T T C G C G C

4: A T C A G G C G G C C A T A G T T G G C G C C A G T G A C C G T A C C A A C C G

5: C C T T G A T G C G G C G C T C G G T C A T C G C T G C A T T G A T C G A G T A

6: G C C A C C G C C G C C G C A A A T G C C C A G C A C G C C A A T G C G T T C T

7: T C A T C C A C A T A G G G G A G C G T T A C G A G G T A G T C G C A G A C C A

8: C G C G G A A A T C C T C G A C G C G C A G T G T C G G G T C T T C G G T A A A

9: A C G T G G T T C G C C G C C G C T G G C A C C C T G G A A G C T G G C G T C G

10: A A G G C G A T G A C G A C G A A A C C T T C C T T G G C C A G C G C C T C G C

11: C A T A C A C G T T C C C C G A T G T T T G C T C C T T G C A G C T G C C G A T

12: C G G A T G C G C G C T G A T G A T G G C G G G A T A T T T C T T G C C T T C G

13: T C G A A G T T C G G C G G G A A G T G G A T G T C G G C T G C G A T A T C C C

14: A A T A C A C A T T C T T G A T C T T G A C G C T T T T C A T G A C A G C T C C

15: G T T C A G G G G G A G G G G G T A A G T T C G C C A G G C C G A A T C G T T G

16: G T A G C C A A G C G G C A A C G A C T C G A A T A T A G A G A G C C G A T T G

17: G A A T T C C G T A A G A T C G C A A T C T G G A C T A C A G T G G T A T C T T

18: C A A A T T G A C A A T G G C A C C T A C A T G G A T C C C T C A C T G C T T C

19: C G T C T C T C G C G T G G T T C G C C C A C G T C G C A C A T C A T C G T A G

20: C T T C A C G A A A G C G G C T G C G G A A A T G G G C G T T T C T C G A G C A

21: A A C C T G T C G C A G A A C G T G A A G G C G C T C G A A C G C C G G T T G A

22: A C G T C A A G C T G C T G T A T C G A A C G A C T C G C G A C A T G T C G C T

23: G A C C G A G G A G G G G C A G C G G C T C T A C G A G G T G T G G T A T C C C

24: G C G C T G G T C G C G G T C G A G C G G A C G G T C G A C G C G C T G C A C G

25: A G G A G C G C G A C G A G C C G T C G G G G T T G A T T C A T T G G G G A G G

26: A G G C G A G T T G A G C G G C G G C A G T T C G C C T G C G T G C G C T G C G

27: C G G C G T C G A C A T C T G A T C C G C A C C A T G G A A A T C C C C G C T C

28: A A T C T T T G G A G C A G G G A T G C G G G G C G A T C A A G A T G G G G A T

29: G C G G G A T G G G G G C G A C G G T G T A T T T C C G C C A G A A G A T T T C

30: G C C G C G G G A G C T C G C G G T G C G T A C G T G C A T G T T C A A A C G C

31: A C G G T G C G C G C A T G G C A G T G G C A G A C T G A T C A A C G C A G C T

32: G G A A G C A T C C G A A G C G C G C G G G C A C G C G T G T C C T C G A C G C

33: G T G G C C T C A C A T G C T G T C G G G T C G G T T C A A G A C C G A A A G C

34: C A C C G A C C G A C G C G C G A G C A A T G C G C T A C G C G G A T C G C G T

35: T C G A C A C G A G C C G C G C G C G A G G C A A G G C C G A C G T A T T C G A

36: T C T T C C A G A G G A A G C C T A T T G G C T C G A G T C G T A G T G C T C G

37: A T A T G G T A G A G C A A C A T G A A T C C C G G G C T A A G T A C A A G A A

38: G T A A C C C G G C A A C G A G T G A G A T T G C G A C G A A T A A A C G C T T

39: C A C C A T G A T C G C G C T C C T G A G T T G G T T G A G G T G A A T T G G A

40: A A G T C G A T T C C T G G G G G A T C A T T C C C G G C A A G G C G C G C A A

<------------------------------------------------------------------------------------------------------------------------>

Basis Last Page

WORKSHEET 35[40, 40]

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z AA AB AC AD AE AF AG AH AI AJ AK AL AM AN

>------------------------------------------------------------------------------------------------------------------------<

1: C A C G A G G C C G A C G A A C G C G T C G C T G A G C G G T T T G A A C A T C

2: G C G C C T G C G T C C G G C C A T A C A T G A C C G A C G G T C A C G C C G A

3: G C A G C A T C G C G A G C A G G A C C T G C A C G T A G A G C G A T T T G A G

4: C A G C C T G G C C A A C C T C A C G G A A C G G T C T T C C T T C G T G T C T

5: C T T G T G T C G T T G T C A C A C C G A T G C A T C G C T G T T C G C G A T G

6: C C G T C G C G C T T C G C G T C G A C G A T C A T C C G G T G A A A T G C T T

7: C G G C G G C C G G C G T G A G C G G C C G T C C G C G C C G C T T G A C G A T

8: G C C C A C G C G G C G T T T G A C G A C C G G C T C G A C G A G C G G C A C G

9: C T C G T G A G A A T C G G G T G G T C G T G C C C G G G C A T C G C C A T C G

10: A C G G C A C C G C G G C G A C G C C G A G C C C C G C C T C G A T C A A G C C

11: G A G C A G G G T C G T C A C G T G G C G C G C T T C G C A T A C G C T C G G C

12: C C C C G C G G C G C C A C G G C G G C C A G C G C C T G G T C G A G C A A C A

13: G G C G G T T C C C G G A A G T C T T G T C C A C C G A C A C G T A A T C G T G

14: C T C G T A C A G T T C G T T C C A G G T A A C G C G C T T C T T G C G C G C G

15: A G C G G A T G G T C G C G G C G G C A G G C A G C G A C G A A C C G C T C C T

16: G G A G C A A C A T C T T G A A C T C G A T G T C G G A T T C C T G G C T G C C

17: C A T G A A G C T C A C G C C G A A A T C G G C T T C G C C G C T G A T G A C G

18: G C G C C C A G C A C C T C G T T C G C G C T C G C G T C C A G C A G C T T G A

19: C C C G G A T G C G C G G A A A G C G C T G A T G A T A G C G C G C G A T G A T

20: G G C C G G C A G A A A G T A G T A G G C G A C C G A G G G C A C G C A C G C G

21: A T G G T C A C A T G G C C C A G G C G G C T C G A C G A C A C G T C G C G A A

22: T G C C G A G C A G C G C C G C A T C G A G A T C G T C G A G C A G C T G T T C

23: G G C G C T C T G G G C G A A C A C G C G G C C G A C C G T G G T G A G C G C G

24: A C G C G A C G C G T G G T G C G C T C G A A C A G G C G C A C G C C G A G C G

25: C T T C C T C G A G C T T G T C G A T C C G G C G A C T C A A C G C G G G C T G

26: G G A A A T G C T G A C C G A T T C C G C G G C C T T G C G G A A A C T G C C C

27: G T T T C C A C G A C C G C G C G A A A C G C C T G C A A G T C G T T C A A G T

28: C G A A G T T G A T C C C C A C G G G C G C G T C T C C C C A T C T C A G A T G

29: G G G C G T A T T T T G C A T G A T T T C G C C G G G C G G C C G C A T C G G C

30: G C G G C A C G C A T T C G C G C C A C C C T C G A T C G C A A C C G C G T G C

31: G T G A G C G T G C G G C C T G G C C G T C G A T C C G C C G C G C G T C G A T

32: G T C G A T G G G G G G C G T C G A G C C T G C G G G C C T T A C G G C G C A A

33: G C A G G C C G C G T G C G G C C A G A T T G G C A T A C A G C G C G C G C A C

34: G C C G A A G G T C C A A G G C G C G A T C T C G G T G C A C A G C C G C A C G

35: G T G T T G A C G A G T G C G C C G A G C G G

36:

37:

38:

39:

40:

<------------------------------------------------------------------------------------------------------------------------>

gen_hw1_2521 Elapsed Time: * 0.177 sec

EXIT FROM EXSAN

A B O U T ExSan

ExSan is essentially a spreadsheet tool built on a novel data structure,

fully coded in C++ conceived using Object Oriented Technology,

console based and capable of handling large matrices, for instance in

Image Processing tasks, Text Mining, Genomic Algos.

It is used for a variety of applications including Pattern Recognition,

Artificial Intelligence, Financial Derivatives Pricing , Digital Forensics

Expertise: Audio, Image & Video and more general Numerical Computing.

From the downloadable file extract executable EXSAN to your desktop.

The very first time ExSan is executed it creates a default input/output

directory c:\exsan

All data files included must be extracted to c:\exsan\exsan_data

The program you are executing uses ExSan as programming tool

Address your request/comments/un-expected results/flaws/errors to:

exsan.plusplus@gmail.com include corresponding c:\exsan\exsan_out(txt) + comment.

This file records the ExSan session.

Thursday, July 23, 2015

Algorithms for DNA Sequencing 001

ExSan++
Thu Jul 23 09:53:12 2015
exsan.plusplus@gmail.com https://twitter.com/#!/ExSan_com
JOB: basic_dna_5312

Data File: c:\exsan\exsan_data\DNA_FA_0001.txt

1st_line TAAACAAGCAGTAGTAATTCCTGCTTTATCAAGATAATTTTTCGACTCATCAGAAATATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGATAAAACTC

size strand 100

total strands 1000

last_line B@DFEFFFGEGGGFGHHHGGFGFGFIHGEGEHGHHGHGGEHBHF@HCIHEHEGHGGGCFGGBHHIHHGHFHHFGDJJDGIFHGKHGGFG>GHDFIFGEED

size strand 100

Basis
WORKSHEET A[10, 10] CHAR
A B C D E F G H I J
>------------------------------<
1: T A A A C A A G C A
2: G T A G T A A T T C
3: C T G C T T T A T C
4: A A G A T A A T T T
5: T T C G A C T C A T
6: C A G A A A T A T C
7: C G A A A G T G T T
8: A A C T T C T G C G
9: T C A T G G A A G C
10: G A T A A A A C T C
<------------------------------>

WORKSHEET B[10, 10] CHAR
A B C D E F G H I J
>------------------------------<
1: A A C A A G C A G T
2: A G T A A T T C C T
3: G C T T T A T C A A
4: G A T A A T T T T T
5: C G A C T C A T C A
6: G A A A T A T A C G
7: A A A G T G T T A A
8: C T T C T G C G T C
9: A T G G A C A C G A
10: A A A A A C T C C C
<------------------------------>

WORKSHEET 999[10, 10]
A B C D E F G H I J
>------------------------------<
1: G C G G C G C A A C
2: C T G T G A C G A C
3: A A A T C T G C T C
4: A A A T T T A T G C
5: G C G C T T C G A T
6: A A A A A T G A T T
7: G G C G T A T C C A
8: A C C T G C A G A G
9: T T T T A T C G C T
10: T C C A T G A C G C
<------------------------------>

WORKSHEET 1000[10, 10]
A B C D E F G H I J
>------------------------------<
1: C G A G C T G C G C
2: A A G G A T A G G T
3: C G A A T T T T C T
4: C A T T T T C C G C
5: C A G C A G T C C A
6: C T T C G A T T T A
7: A T T C G T A A A C
8: A A G C A G T A G T
9: A A T T C C T G C T
10: T T A T C A A G A T
<------------------------------>

Qualities
WORKSHEET A[10, 10] PIX
A B C D E F G H I J
>------------------------------<
1: 33 31 35 37 36 37 37 37 38 36
2: 38 38 38 39 36 39 38 39 38 39
3: 38 38 38 38 39 40 37 38 37 40
4: 37 39 40 34 37 38 39 38 39 38
5: 41 38 39 37 38 39 38 40 39 36
6: 39 38 38 39 41 38 37 36 37 39
7: 38 39 36 38 38 39 39 38 39 40
8: 37 38 37 38 35 40 37 38 38 37
9: 38 38 38 37 39 38 38 38 39 38
10: 38 38 32 38 40 37 38 38 34 38
<------------------------------>

WORKSHEET B[10, 10] PIX
A B C D E F G H I J
>------------------------------<
1: 28 31 31 34 36 33 37 31 33 38
2: 33 38 21 38 37 16 36 27 15 19
3: 34 18 36 22 36 13 24 38 28 39
4: 27 39 25 39 39 26 39 33 39 26
5: 38 21 24 37 22 11 22 35 38 7
6: 7 36 38 23 32 23 11 12 20 12
7: 23 11 30 11 11 11 32 36 29 34
8: 11 33 30 11 11 11 21 19 3 32
9: 34 6 10 6 28 6 10 19 6 18
10: 9 19 10 36 18 17 17 9 6 7
<------------------------------>

WORKSHEET 999[10, 10]
A B C D E F G H I J
>------------------------------<
1: 14 31 35 34 31 33 37 35 38 33
2: 38 31 38 21 36 29 32 33 38 39
3: 38 37 37 38 35 40 38 38 37 37
4: 36 39 37 35 39 38 11 37 33 36
5: 38 34 36 35 31 39 38 37 39 36
6: 32 36 35 39 38 38 22 33 37 32
7: 23 22 30 38 22 30 37 36 35 37
8: 39 29 35 38 21 40 33 38 38 37
9: 19 34 38 29 34 38 38 36 35 35
10: 38 38 38 17 18 24 30 34 26 31
<------------------------------>

WORKSHEET 1000[10, 10]
A B C D E F G H I J
>------------------------------<
1: 33 31 35 37 36 37 37 37 38 36
2: 38 38 38 37 38 39 39 39 38 38
3: 37 38 37 38 37 40 39 38 36 38
4: 36 39 38 39 39 38 39 38 38 36
5: 39 33 39 37 31 39 34 40 39 36
6: 39 36 38 39 38 38 38 34 37 38
7: 38 33 39 39 40 39 39 38 39 37
8: 39 39 37 38 35 41 41 35 38 40
9: 37 39 38 42 39 38 38 37 38 29
10: 38 39 35 37 40 37 38 36 36 35
<------------------------------>

Total counter = 100000
n_A = 28426 n_C = 21890 n_G = 19147 n_T = 30531 n_N = 6 total: 100000 ***n_GC = 41037

% A: 28.43 C: 21.89 G: 19.15 T: 30.53 N: 0.006

check-sum-> 1

Qualities min = 0 max = 43 range: 43

delta_Q: 43

Histogram of Qualities( 0 <--> 43 ):

0.046% 0 - 4 :

0.552% 4 - 8 :

1.472% 8 - 12 : *

1.487% 12 - 17 : *

1.861% 17 - 21 : *

2.231% 21 - 25 : **

9.051% 25 - 30 : *********

63.4% 30 - 34 : ***************************************************************

19.83% 34 - 38 : *******************

0.07% 38 - 43 :

Sequencing by Synthesis
DNA Polymerase basic_dna_5312 Elapsed Time: * 0.837 sec

EXIT FROM EXSAN

A B O U T E x S a n

ExSan is essentially a spreadsheet tool built on a novel data structure,
fully coded in C++11 conceived using Object Oriented Technology,
console based and capable of handling large matrices, for instance in
Image Processing tasks, Text Mining.
It is used for a variety of applications including Pattern Recognition,
Artificial Intelligence, Financial Derivatives Pricing , Digital Forensics
Expertise: Audio, Image & Video and more general Numerical Computing.
From the downloadable file extract executable EXSAN to your desktop.
The very first time ExSan is executed it creates a default input/output
directory c:\exsan
All data files included must be extracted to c:\exsan\exsan_data
The program you are executing uses ExSan as programming tool
Address your request/comments/un-expected results/flaws/errors to:

exsan.plusplus@gmail.com include corresponding c:\exsan\exsan_out(txt) + comment.

This file records the ExSan session.