Genome Assembly Programming Week 2- Assembling Genomes Using de Bruijn Graphs Solution

Course: Genome Assembly Programming Challenge (Course 6 out of 6)
Specialization: Data Structures and Algorithms
Programming Assignment 2:
Assembling Genomes Using de Bruijn Graphs
Introduction
Welcome to the second programming assignment of the Genome Assembly Programming Challenge! In this assignment, you will be practicing assembling the phi X174 genome using de Bruijn graphs.
Passing Criteria: 2 out of 4
Passing this programming assignment requires passing at least 2 out of 4 code problems from this assignment. In turn, passing a code problem requires implementing a solution that passes all the tests for this problem in the grader and does so under the time and memory limits specified in the problem statement.
Contents
1 Dataset Problem: Puzzle Assembly 3
2 Problem: Finding an Eulerian Cycle in Directed Graph 5
3 Problem: Finding a k-Universal Circular String 8
4 Dataset Problem: Assembling the phi X174 Genome from its k-mer Composition 9
5 General Instructions and Recommendations on Solving Algorithmic Problems 10
5.1 Reading the Problem Statement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
5.2 Designing an Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
5.3 Implementing Your Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
5.4 Compiling Your Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
5.5 Testing Your Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
5.6 Submitting Your Program to the Grading System . . . . . . . . . . . . . . . . . . . . . . . . . 12
5.7 Debugging and Stress Testing Your Program . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
6 Frequently Asked Questions 13
6.1 I submit the program, but nothing happens. Why? . . . . . . . . . . . . . . . . . . . . . . . . 13 6.2 I submit the solution only for one problem, but all the problems in the assignment are graded.
Why? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
6.3 What are the possible grading outcomes, and how to read them? . . . . . . . . . . . . . . . . 13
6.4 How to understand why my program fails and to fix it? . . . . . . . . . . . . . . . . . . . . . 14
6.5 Why do you hide the test on which my program fails? . . . . . . . . . . . . . . . . . . . . . . 14
6.7 My implementation always fails in the grader, though I already tested and stress tested it a lot. Would not it be better if you give me a solution to this problem or at least the test cases that you use? I will then be able to fix my code and will learn how to avoid making mistakes. Otherwise, I do not feel that I learn anything from solving this problem. I am just stuck. . . . 15
1 Dataset Problem: Puzzle Assembly
In dataset problems, you solution is going to be tested against a single dataset as opposed to problems in the previous classes in this specialization. For this reason, there is no Constraints section in the problem description below. The sample section shows just a similar dataset. Your program is not going to be tested on this dataset.
Problem Introduction
In this problem, we will consider a square puzzle consisting of n-by-n square pieces, where each square piece has a single color on each of its four edges. Given a set of n2 square pieces, your task is to find a way to place them in an n-by-n grid such that all adjacent edges of square pieces are of the same color.
Problem Description
Task. Let each square piece be defined by the four colors of its four edges, in the format (up,left,down,right). Below is an example of a square piece:

Let a “valid placement” be defined as a placement of n2 square pieces onto an n-by-n grid such that all “outer edges” (i.e., edges that border no other square pieces), and only these edges, are black, and for all edges that touch an edge in another square piece, the two touching edges are the same color. Below is an example of a “valid placement” on a 3-by-3 square grid:

You will be given 25 square pieces in the format described above, and you will need to return a “valid placement” of them onto a 5-by-5 grid. To simplify the problem, we guarantee that all of the square pieces are given to you in the correct orientation (i.e., you will not need to rotate any of the pieces to have them fit in a “valid placement”). For example, the square (green,black,red,blue) and the similar square (black,red,blue,green) are not equivalent in this problem.
Dataset. Each line of the input contains a single square piece, in the format described above: (up,left,down,right). You will be given 25 such pieces in total (so 25 lines of input). Note that all “outer edges” (i.e., edges that border no other square pieces on the puzzle) are black, and none of the “inner edges” (i.e., edges not on the outside border of the puzzle) are black.
Output. Output a “valid placement" of the inputted pieces in a 5-by-5 grid. Specifically, your output should be exactly 5 lines long (representing the 5 rows of the grid), and on each line of your output, you should output 5 square pieces in the exact format described, (up,left,down,right), separated by semicolons. There should be no space characters at all in your output.
Time Limits.
language C C++ Java Python C# Haskell JavaScript Ruby Scala
time (sec) 10 10 15 50 15 20 50 50 30
Memory Limit. 512MB.
Sample 1.
Input:
(yellow,black,black,blue)
(blue,blue,black,yellow)
(orange,yellow,black,black)
(red,black,yellow,green)
(orange,green,blue,blue)
(green,blue,orange,black) (black,black,red,red)
(black,red,orange,purple) (black,purple,green,black)
Output:
(black,black,red,red);(black,red,orange,purple);(black,purple,green,black)
(red,black,yellow,green);(orange,green,blue,blue);(green,blue,orange,black)
(yellow,black,black,blue);(blue,blue,black,yellow);(orange,yellow,black,black)
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2 Problem: Finding an Eulerian Cycle in Directed Graph
Problem Introduction
A cycle in a graph is called Eulerian if it traverses each edge of the graph exactly once. Assuming that there are no isolated vertices in a graph, it contains an Eulerian cycle if and only if it is strongly connected and for each vertex, its in-degree is equal to its out-degree. Recall from the lectures that a (circular) genome spells an Eulerian cycles in the de Bruijn graph constructed on all k-mers of the genome.
Problem Description
Task. Given a directed graph, find an Eulerian cycle in the graph or report that none exists.
Constraints. 1 ≤ n ≤ 104; n ≤ m ≤ 105; 1 ≤ u,v ≤ n.
Time Limits.
language C C++ Java Python C# Haskell JavaScript Ruby Scala
time (sec) 1 1 1.5 5 1.5 2 5 5 3
Memory Limit. 512MB.
Sample 1.
Input:
3 4
2 3
2 2
1 2
3 1
Output:
1
1 2 2 3
Explanation:

There is an Eulerian cycle in this graph: 1 → 2 → 2 → 3 → 1.
Sample 2.
Input:
3 4
1 3
2 3
1 2
3 1
Output:
0
Explanation:

There is no Eulerian cycle in this graph since, for example, the vertex 1 is imbalanced: its out-degree is higher that its in-degree.
Sample 3.
Input:
4 7
1 2
2 1
1 4
4 1
2 4
3 2
4 3
Output:
1
4 3 2 4 1 2 1
Explanation:

There is an Eulerian cycle in this graph: 4 → 3 → 2 → 4 → 1 → 2 → 1 → 4.
Sample 4.
Input:
4 7
2 3
3 4
1 4
3 1
4 2
2 3
4 2
Output:
1 2 3 4 2 3 1 4
Explanation:

There is an Eulerian cycle in this graph: 2 → 3 → 4 → 2 → 3 → 1 → 4.
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3 Problem: Finding a k-Universal Circular String
Problem Introduction
A k-universal circular string is a circular string that contains every possible k-mer constructed over a given alphabet.
Problem Description
Task. Find a k-universal circular binary string.
Input Format. An integer k.
Constraints. 4 ≤ k ≤ 14.
language C C++ Java Python C# Haskell JavaScript Ruby Scala
time (sec) 1 1 1.5 5 1.5 2 5 5 3
Memory Limit. 512MB.
Sample 1.
Input:
4
Output:
0000110010111101
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4 Dataset Problem: Assembling the phi X174 Genome from its k-mer Composition
In dataset problems, you solution is going to be tested against a single dataset as opposed to problems in the previous classes in this specialization. For this reason, there is no Constraints section in the problem description below. The sample section shows just a similar dataset. Your program is not going to be tested on this dataset.
Problem Introduction
In this challenge, you will be given the task of performing Genome Assembly based on the “k-mer composition” of the genome.
Problem Description
Task. Let the “k-mer composition” of a string Text be defined as the list of every k-mer in Text (in any order). For example, the 3-mer composition of the circular string ACGTA is [ACG, CGT, GTA, TAC, AAC]. Given the k-mer composition of some unknown string, perform the task of Genome Assembly and return the circular genome from which the k-mers came. In other words, return a string whose k-mer composition is equal to the given list of k-mers.
Dataset. Each of the 5396 lines of the input contains a single k-mer. The k-mers are given to you in alphabetical order because their true order is hidden from you. Each k-mer is 10 nucleotides long.
Output. Output the assembled genome on a single line.
Time Limits.
language C C++ Java Python C# Haskell JavaScript Ruby Scala
time (sec) 3 3 4.5 15 4.5 6 15 15 9
Memory Limit. 512MB.
Sample 1.
Input:
AAC ACG CGT
GTA
TAA
Output:
ACGTA
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5 General Instructions and Recommendations on Solving Algorithmic Problems
Your main goal in an algorithmic problem is to implement a program that solves a given computational problem in just few seconds even on massive datasets. Your program should read a dataset from the standard input and write an answer to the standard output.
Below we provide general instructions and recommendations on solving such problems. Before reading them, go through readings and screencasts in the first module that show a step by step process of solving two algorithmic problems: link.
5.1 Reading the Problem Statement
You start by reading the problem statement that contains the description of a particular computational task as well as time and memory limits your solution should fit in, and one or two sample tests. In some problems your goal is just to implement carefully an algorithm covered in the lectures, while in some other problems you first need to come up with an algorithm yourself.
5.2 Designing an Algorithm
If your goal is to design an algorithm yourself, one of the things it is important to realize is the expected running time of your algorithm. Usually, you can guess it from the problem statement (specifically, from the subsection called constraints) as follows. Modern computers perform roughly 108–109 operations per second. So, if the maximum size of a dataset in the problem description is n = 105, then most probably an algorithm with quadratic running time is not going to fit into time limit (since for n = 105, n2 = 1010) while a solution with running time O(nlogn) will fit. However, an O(n2) solution will fit if n is up to 103 = 1000, and if n is at most 100, even O(n3) solutions will fit. In some cases, the problem is so hard that we do not know a polynomial solution. But for n up to 18, a solution with O(2nn2) running time will probably fit into the time limit.
To design an algorithm with the expected running time, you will of course need to use the ideas covered in the lectures. Also, make sure to carefully go through sample tests in the problem description.
5.3 Implementing Your Algorithm
When you have an algorithm in mind, you start implementing it. Currently, you can use the following programming languages to implement a solution to a problem: C, C++, C#, Haskell, Java, JavaScript, Python2, Python3, Ruby, Scala. For all problems, we will be providing starter solutions for C++, Java, and Python3. If you are going to use one of these programming languages, use these starter files. For other programming languages, you need to implement a solution from scratch.
5.4 Compiling Your Program
For solving programming assignments, you can use any of the following programming languages: C, C++, C#, Haskell, Java, JavaScript, Python2, Python3, Ruby, and Scala. However, we will only be providing starter solution files for C++, Java, and Python3. The programming language of your submission is detected automatically, based on the extension of your submission.
We have reference solutions in C++, Java and Python3 which solve the problem correctly under the given restrictions, and in most cases spend at most 1/3 of the time limit and at most 1/2 of the memory limit. You can also use other languages, and we’ve estimated the time limit multipliers for them, however, we have no guarantee that a correct solution for a particular problem running under the given time and memory constraints exists in any of those other languages.
• C (gcc 5.2.1). File extensions: .c. Flags:
gcc - pipe -O2 - std=c11 <filename> -lm
• C++ (g++ 5.2.1). File extensions: .cc, .cpp. Flags:
g++ - pipe -O2 - std=c++14 <filename> -lm
mcs
• Haskell (ghc 7.8.4). File extensions: .hs. Flags:
ghc -O2
• Java (Open JDK 8). File extensions: .java. Flags:
javac - encoding UTF-8
java -Xmx1024m
• JavaScript (Node v6.3.0). File extensions: .js. Flags:
nodejs
• Python 2 (CPython 2.7). File extensions: .py2 or .py (a file ending in .py needs to have a first linewhich is a comment containing “python2”). No flags:
python2
• Python 3 (CPython 3.4). File extensions: .py3 or .py (a file ending in .py needs to have a first linewhich is a comment containing “python3”). No flags:
python3
• Ruby (Ruby 2.1.5). File extensions: .rb.
ruby
• Scala (Scala 2.11.6). File extensions: .scala.
scalac
5.5 Testing Your Program
When your program is ready, you start testing it. It makes sense to start with small datasets (for example, sample tests provided in the problem description). Ensure that your program produces a correct result.
You then proceed to checking how long does it take your program to process a massive dataset. For this, it makes sense to implement your algorithm as a function like solve(dataset) and then implement an additional procedure generate() that produces a large dataset. For example, if an input to a problem is a sequence of integers of length 1 ≤ n ≤ 105, then generate a sequence of length exactly 105, pass it to your solve() function, and ensure that the program outputs the result quickly.
Also, check the boundary values. Ensure that your program processes correctly sequences of size n = 1,2,105. If a sequence of integers from 0 to, say, 106 is given as an input, check how your program behaves when it is given a sequence 0,0,...,0 or a sequence 106,106,...,106. Check also on randomly generated data. For each such test check that you program produces a correct result (or at least a reasonably looking result).
In the end, we encourage you to stress test your program to make sure it passes in the system at the first attempt. See the readings and screencasts from the first week to learn about testing and stress testing: link.
5.6 Submitting Your Program to the Grading System
When you are done with testing, you submit your program to the grading system. For this, you go the submission page, create a new submission, and upload a file with your program. The grading system then compiles your program (detecting the programming language based on your file extension, see Subsection 5.4) and runs it on a set of carefully constructed tests to check that your program always outputs a correct result and that it always fits into the given time and memory limits. The grading usually takes no more than a minute, but in rare cases when the servers are overloaded it might take longer. Please be patient. You can safely leave the page when your solution is uploaded.
5.7 Debugging and Stress Testing Your Program
If your program failed, you will need to debug it. Most probably, you didn’t follow some of our suggestions from the section 5.5. See the readings and screencasts from the first week to learn about debugging your program: link.
You are almost guaranteed to find a bug in your program using stress testing, because the way these programming assignments and tests for them are prepared follows the same process: small manual tests, tests for edge cases, tests for large numbers and integer overflow, big tests for time limit and memory limit checking, random test generation. Also, implementation of wrong solutions which we expect to see and stress testing against them to add tests specifically against those wrong solutions.
Go ahead, and we hope you pass the assignment soon!
6 Frequently Asked Questions
6.1 I submit the program, but nothing happens. Why?
You need to create submission and upload the file with your solution in one of the programming languages C, C++, Java, or Python (see Subsections 5.3 and 5.4). Make sure that after uploading the file with your solution you press on the blue “Submit” button in the bottom. After that, the grading starts, and the submission being graded is enclosed in an orange rectangle. After the testing is finished, the rectangle disappears, and the results of the testing of all problems is shown to you.
6.2 I submit the solution only for one problem, but all the problems in the assignment are graded. Why?
Each time you submit any solution, the last uploaded solution for each problem is tested. Don’t worry: this doesn’t affect your score even if the submissions for the other problems are wrong. As soon as you pass the sufficient number of problems in the assignment (see in the pdf with instructions), you pass the assignment. After that, you can improve your result if you successfully pass more problems from the assignment. We recommend working on one problem at a time, checking whether your solution for any given problem passes in the system as soon as you are confident in it. However, it is better to test it first, please refer to the reading about stress testing: link.
6.3 What are the possible grading outcomes, and how to read them?
Good job! Hurrah! Your solution passed, and you get a point!
Wrong answer. Your solution has output incorrect answer for some test case. If it is a sample test case from the problem statement, or if you are solving Programming Assignment 1, you will also see the input data, the output of your program and the correct answer. Otherwise, you won’t know the input, the output, and the correct answer. Check that you consider all the cases correctly, avoid integer overflow, output the required white space, output the floating point numbers with the required precision, don’t output anything in addition to what you are asked to output in the output specification of the problem statement. See this reading on testing: link.
Time limit exceeded. Your solution worked longer than the allowed time limit for some test case. If it is a sample test case from the problem statement, or if you are solving Programming Assignment 1, you will also see the input data and the correct answer. Otherwise, you won’t know the input and the correct answer. Check again that your algorithm has good enough running time estimate. Test your program locally on the test of maximum size allowed by the problem statement and see how long it works. Check that your program doesn’t wait for some input from the user which makes it to wait forever. See this reading on testing: link.
Memory limit exceeded. Your solution used more than the allowed memory limit for some test case. If it is a sample test case from the problem statement, or if you are solving Programming Assignment 1,
you will also see the input data and the correct answer. Otherwise, you won’t know the input and the correct answer. Estimate the amount of memory that your program is going to use in the worst case and check that it is less than the memory limit. Check that you don’t create too large arrays or data structures. Check that you don’t create large arrays or lists or vectors consisting of empty arrays or empty strings, since those in some cases still eat up memory. Test your program locally on the test of maximum size allowed by the problem statement and look at its memory consumption in the system.
Cannot check answer. Perhaps output format is wrong. This happens when you output something completely different than expected. For example, you are required to output word “Yes” or “No”, but you output number 1 or 0, or vice versa. Or your program has empty output. Or your program outputs not only the correct answer, but also some additional information (this is not allowed, so please follow exactly the output format specified in the problem statement). Maybe your program doesn’t output anything, because it crashes.
Unknown signal 6 (or 7, or 8, or 11, or some other). This happens when your program crashes. It can be because of division by zero, accessing memory outside of the array bounds, using uninitialized variables, too deep recursion that triggers stack overflow, sorting with contradictory comparator, removing elements from an empty data structure, trying to allocate too much memory, and many other reasons. Look at your code and think about all those possibilities. Make sure that you use the same compilers and the same compiler options as we do. Try different testing techniques from this reading: link.
Internal error: exception... Most probably, you submitted a compiled program instead of a source code.
Grading failed. Something very wrong happened with the system. Contact Coursera for help or write in the forums to let us know.
6.4 How to understand why my program fails and to fix it?
If your program works incorrectly, it gets a feedback from the grader. For the Programming Assignment 1, when your solution fails, you will see the input data, the correct answer and the output of your program in case it didn’t crash, finished under the time limit and memory limit constraints. If the program crashed, worked too long or used too much memory, the system stops it, so you won’t see the output of your program or will see just part of the whole output. We show you all this information so that you get used to the algorithmic problems in general and get some experience debugging your programs while knowing exactly on which tests they fail.
However, in the following Programming Assignments throughout the Specialization you will only get so much information for the test cases from the problem statement. For the next tests you will only get the result: passed, time limit exceeded, memory limit exceeded, wrong answer, wrong output format or some form of crash. We hide the test cases, because it is crucial for you to learn to test and fix your program even without knowing exactly the test on which it fails. In the real life, often there will be no or only partial information about the failure of your program or service. You will need to find the failing test case yourself. Stress testing is one powerful technique that allows you to do that. You should apply it after using the other testing techniques covered in this reading.
6.5 Why do you hide the test on which my program fails?
Often beginner programmers think by default that their programs work. Experienced programmers know, however, that their programs almost never work initially. Everyone who wants to become a better programmer needs to go through this realization.
When you are sure that your program works by default, you just throw a few random test cases against it, and if the answers look reasonable, you consider your work done. However, mostly this is not enough. To make one’s programs work, one must test them really well. Sometimes, the programs still don’t work although you tried really hard to test them, and you need to be both skilled and creative to fix your bugs. Solutions to algorithmic problems are one of the hardest to implement correctly. That’s why in this Specialization you will gain this important experience which will be invaluable in the future when you write programs which you really need to get right.
It is crucial for you to learn to test and fix your programs yourself. In the real life, often there will be no or only partial information about the failure of your program or service. Still, you will have to reproduce the failure to fix it (or just guess what it is, but that’s rare, and you will still need to reproduce the failure to make sure you have really fixed it). When you solve algorithmic problems, it is very frequent to make subtle mistakes. That’s why you should apply the testing techniques described in this reading to find the failing test case and fix your program.
(link).
6.7 My implementation always fails in the grader, though I already tested and stress tested it a lot. Would not it be better if you give me a solution to this problem or at least the test cases that you use? I will then be able to fix my code and will learn how to avoid making mistakes. Otherwise, I do not feel that I learn anything from solving this problem. I am just stuck.
First of all, you always learn from your mistakes.
The process of trying to invent new test cases that might fail your program and proving them wrong is often enlightening. This thinking about the invariants which you expect your loops, ifs, etc. to keep and proving them wrong (or right) makes you understand what happens inside your program and in the general algorithm you’re studying much more.
Also, it is important to be able to find a bug in your implementation without knowing a test case and without having a reference solution. Assume that you designed an application and an annoyed user reports that it crashed. Most probably, the user will not tell you the exact sequence of operations that led to a crash. Moreover, there will be no reference application. Hence, once again, it is important to be able to locate a bug in your implementation yourself, without a magic oracle giving you either a test case that your program fails or a reference solution. We encourage you to use programming assignments in this class as a way of practicing this important skill.