Introduction Hack session activities are small weekly programming...
Question
Introduction
Hack session activities are small weekly programming assignments intended to get you started on full programming assignments. Collaboration is allowed and, in fact,highly encouraged. You may start on the activity before your hack session, but during the hack session you must either be actively working on this activity orhelping others work on the activity. You are graded using the same rubric as assignments so documentation, style,design and correctness are all important.
Exercises
To get more practice working with files, you will write several functions that involve operations on files. In particular, implement the following functions.
1. Write a function that, given a file path/name as a string opens the file and returnsits entire contents as a single string. Any endline characters should be preserved.
char *getFileContents(const char *filePath);
2. Write a function that, given a file path/name as a string opens the file and returns the contents of the file as an array of strings. Each element in the array should correspond to a line in the file. Any end line character should be chomped out and not included.
char **getFileLines(const char *filePath, int *numLines);
Protein Translation
DNA is a molecule that encode genetic information. A DNA sequence is a string of nucleotides represented as letters A, T, C, and G (representing the nucleobases adenine ,thymine, cytosine, and guanine respectively). Protein sequencing in an organism consists of a two step process. First the DNA is translated into RNA by replacing each thymine nucleotide with uracil (U). Then, the RNA sequence is translated into a protein (a sequence of amino acids) according to the following rules. The RNA sequence is processed 3 bases at a time called acodon. Each codon is translatedinto a single amino acid according to known encoding rules. There are 20 such aminoacids, each represented by a single letter in
(A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y)
Because there are 43= 64 possible codons but only 20 amino acids, some codons translate to the same amino acid.The rules for translating trigrams are complex, but we’ve simplified the process by providing a utility function,rnaToProteinwhich takes an RNA codon (as a string) and returns its protein (as a singlechar). If you provide it an invalid sequence, it will return\0the null character.In addition, the trigrams UAA, UAG, and UGA are special markers that indicate a (premature) end to the protein sequencing (there may be additional nucleotides left in the RNA sequence, but they are ignored and the translation ends). The function we’ve provided will return a lower-case character for any of these three trigrams.
As an example, suppose we start with the DNA sequence AAAT T CCGCGT ACCC;
it would be encoded into RNA as AAAUUCCGCGUACCC; and into an amino acid sequence KF RV P. You will write a program that takes two command line arguments. The first is an inputfile containing a DNA sequence and the second is the name of the output file in whichyou’ll place the translated protein sequence. As an example, your program should be executable from the command line as:~>./a.out dnaInputFile.txt protein.txt
The input file may contain irrelevant white space characters to avoid very long lines. You will need to ignore any white space characters when you process the data. Place all your code in a file named proteinTranslator.c.
Instructions
•For the exercises, place all your function prototypes into a file namedfile_utils.hand and their definitions in a file namedfile_utils.c. In addition, you’ll wantto create a main test driver program that demonstrates at least 3 cases per functionto verify their output. You need not hand it in, however.
•Code for themrnaToProteinmfunction as well as a demonstration on how to use it has been provided. However, you only need to handinproteinTranslator.c(and anything else thatyou may find helpful).
•You are encouraged to collaborate any number of students before, during, and afteryour scheduled hack session.
•You may (in fact are encouraged) to define any additional “helper” functions that may help you.
•Include the name(s) of everyone who worked together on this activity in your sourcefile’s header.
•Turn in all of your files via webhandin, making sure that it runs and executes correctly in the webgrader. Each individual student will need to hand in their own copy and will receive their own individual grade.
Hack session activities are small weekly programming assignments intended to get you started on full programming assignments. Collaboration is allowed and, in fact,highly encouraged. You may start on the activity before your hack session, but during the hack session you must either be actively working on this activity orhelping others work on the activity. You are graded using the same rubric as assignments so documentation, style,design and correctness are all important.
Exercises
To get more practice working with files, you will write several functions that involve operations on files. In particular, implement the following functions.
1. Write a function that, given a file path/name as a string opens the file and returnsits entire contents as a single string. Any endline characters should be preserved.
char *getFileContents(const char *filePath);
2. Write a function that, given a file path/name as a string opens the file and returns the contents of the file as an array of strings. Each element in the array should correspond to a line in the file. Any end line character should be chomped out and not included.
char **getFileLines(const char *filePath, int *numLines);
Protein Translation
DNA is a molecule that encode genetic information. A DNA sequence is a string of nucleotides represented as letters A, T, C, and G (representing the nucleobases adenine ,thymine, cytosine, and guanine respectively). Protein sequencing in an organism consists of a two step process. First the DNA is translated into RNA by replacing each thymine nucleotide with uracil (U). Then, the RNA sequence is translated into a protein (a sequence of amino acids) according to the following rules. The RNA sequence is processed 3 bases at a time called acodon. Each codon is translatedinto a single amino acid according to known encoding rules. There are 20 such aminoacids, each represented by a single letter in
(A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y)
Because there are 43= 64 possible codons but only 20 amino acids, some codons translate to the same amino acid.The rules for translating trigrams are complex, but we’ve simplified the process by providing a utility function,rnaToProteinwhich takes an RNA codon (as a string) and returns its protein (as a singlechar). If you provide it an invalid sequence, it will return\0the null character.In addition, the trigrams UAA, UAG, and UGA are special markers that indicate a (premature) end to the protein sequencing (there may be additional nucleotides left in the RNA sequence, but they are ignored and the translation ends). The function we’ve provided will return a lower-case character for any of these three trigrams.
As an example, suppose we start with the DNA sequence AAAT T CCGCGT ACCC;
it would be encoded into RNA as AAAUUCCGCGUACCC; and into an amino acid sequence KF RV P. You will write a program that takes two command line arguments. The first is an inputfile containing a DNA sequence and the second is the name of the output file in whichyou’ll place the translated protein sequence. As an example, your program should be executable from the command line as:~>./a.out dnaInputFile.txt protein.txt
The input file may contain irrelevant white space characters to avoid very long lines. You will need to ignore any white space characters when you process the data. Place all your code in a file named proteinTranslator.c.
Instructions
•For the exercises, place all your function prototypes into a file namedfile_utils.hand and their definitions in a file namedfile_utils.c. In addition, you’ll wantto create a main test driver program that demonstrates at least 3 cases per functionto verify their output. You need not hand it in, however.
•Code for themrnaToProteinmfunction as well as a demonstration on how to use it has been provided. However, you only need to handinproteinTranslator.c(and anything else thatyou may find helpful).
•You are encouraged to collaborate any number of students before, during, and afteryour scheduled hack session.
•You may (in fact are encouraged) to define any additional “helper” functions that may help you.
•Include the name(s) of everyone who worked together on this activity in your sourcefile’s header.
•Turn in all of your files via webhandin, making sure that it runs and executes correctly in the webgrader. Each individual student will need to hand in their own copy and will receive their own individual grade.
Solution Preview
These solutions may offer step-by-step problem-solving explanations or good writing examples that include modern styles of formatting and construction of bibliographies out of text citations and references.
Students may use these solutions for personal skill-building and practice.
Unethical use is strictly forbidden.
#include"file_utils.h"
char *getFileContents(const char *filePath){
ifstream inFile;
inFile.open(filePath,ios::in);
if(!inFile.is_open()){
cout<<"error can not open words.txt file\n";
system("pause");
exit(1);
}
inFile.seekg(0,ios::end);
int size = inFile.tellg();
string content = "";
char temp;
int index = 0 , i ;
inFile.seekg(0,ios::beg);
string str;
while(!inFile.eof()){
inFile.get(temp);
if(inFile.fail()) break;
content += temp;
}
char const *data = content.data();
string ddd = data;
char *d = new char[strlen(data)];
for( i = 0 ; i < strlen(data) ; i++){
strcpy((d+i),(data+i));
}
return d ;
}
char **getFileLines(const char *filePath, int *numLines)
{
ifstream inFile;
inFile.open(filePath,ios::in);
if(!inFile.is_open
char *getFileContents(const char *filePath){
ifstream inFile;
inFile.open(filePath,ios::in);
if(!inFile.is_open()){
cout<<"error can not open words.txt file\n";
system("pause");
exit(1);
}
inFile.seekg(0,ios::end);
int size = inFile.tellg();
string content = "";
char temp;
int index = 0 , i ;
inFile.seekg(0,ios::beg);
string str;
while(!inFile.eof()){
inFile.get(temp);
if(inFile.fail()) break;
content += temp;
}
char const *data = content.data();
string ddd = data;
char *d = new char[strlen(data)];
for( i = 0 ; i < strlen(data) ; i++){
strcpy((d+i),(data+i));
}
return d ;
}
char **getFileLines(const char *filePath, int *numLines)
{
ifstream inFile;
inFile.open(filePath,ios::in);
if(!inFile.is_open
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