[SOLVED] C: CSC209-Assignment 1: Using the Shell and Intro C

PART 1. USING SHELL

COMMANDS

In this part we are going to use existing command-line tools to extract some meaningful information from files. To accomplish that you would need to review some shell commands. We have learned most of them in class, but you may need to find out some additional options, which you can do by reading the relevant man pages. At first, you may find reading man pages difficult because they are written for a technical audience, but it will pay off in the future because you will be able to access the complete and correct information about every command.

Hint: commands for part 1

head : extracts first n rows from a text file. Default value is 10 rows, find out how to specify the number of rows as a parameter.

tail : same as head only for last n rows.

cut cut: cuts out a number of columns from a tabular file. We need to know how to specify column numbers and how to specify a field delimiter.

grep : we need to know how to match the entire word

sort : we need to know what parameters we need to perform numeric sort, sorting by fields and specifying field delimiters, sorting more than one file.

uniq : used for both removing and finding duplicate lines in a file.

wc : we are interested in the option which

of the site length.
2. The ratio of observed CG substrings to expected is at least 60%.

You will declare and define separate functions to compute these two values. The expected number of CG patterns is calculated for each region as (count (C) * count (G))/N, where N is the total number of characters in the site considered. The observed is just total count of CGs: count (CG). So to find the observed to expected ratio we divide observed by expected.

Your goal is to find and report all CpG islands in a given DNA sequence. Sample file dna.txt represents a short DNA sequence from a genome of Norway rat.

UPDATE: Because it turned out that almoust entire input sequence in dna.txt comes from a CpG island, to ensure that your program handles all different usecases, please also test it on the DNA sequence of Human chromosome 21 which you can download from here (chr21.fa.gz). You do not need to modify your code, just use a different input file. If you also count the total number of characters in all CpG islands, you will see that CpG islands cover only a small portion of a genome.

The input is given in the widely used FASTA format, and the first step is to convert the input into a char array. As we did not learn how to read files yet, the code for reading all bytes from a file and converting them into an array of valid DNA characters is provided.

Once you have your character array, you can process each window of length 200 characters to determine whether it is a part of CpG island.

You slide the window by one character at each iteration. To simplify the task, and because your sequence is small, we will use the following algorithm.

for each window of length 200, calculate if it belongs to a CpG island
if it does, set the corresponding 200 entries in array valid_cpg_positions to 1

when the entire sequence has been processed, combine valid CpG sites into larger islands looping over

 valid_cpg_positions

print the start and end position of each CpG island that you discovered

Sample output:

The output consists of the table in the following format:

CpG islandCpG islandnumislands

104..509size=406596..924size=3292

Each column is separated by a tab

Submit:

Source code in file cpg.c and the output of your program in file cpg_output.txt.

Starter code

#include <stdio.h> #include <stdlib.h>

//function declarations

int valid_chars_count (char *input, int size);

)){

int valid_char (char c);

int main (int argc, char *argv[]) {
char * inputfile_name=argv[1];
FILE * input_fp;
char *input_buffer; //stores all bytes in the i

nput file
char *sequence; //char array holding the fin

al cleaned DNA sequence

int *valid_cpg_positions; //array of all positi ons in sequence

int input_len, seq_len; int i, j;

int r;
//open the file

if ( !(input_fp= fopen ( inputfile_name , rb )

printf(Could not open file %s for r eading input lines
, inputfile_name);

return (-1); }

//compute total number of characters in the input file

fseek (input_fp, 0, SEEK_END); input_len=ftell (input_fp);
rewind (input_fp);
printf (total bytes in file: %d
, input_len);

//allocate an array to hold these characters

input_buffer = (char*) malloc (input_len+1);

//read file content into the input buffer

r = fread (input_buffer, 1, input_len, input_f

p);

printf (read characters %d
, r); if (r != input_len) {

printf(Reading error
);

return (-1); }

//add terminating character

input_buffer [input_len] =;

//determine total number of valid DNA char acters

//and allocate array of chars to hold them

seq_len = valid_chars_count (input_buffer, i nput_len);

printf (total characters %d total valid char acters %d
, input_len, seq_len);

sequence = (char*) malloc (seq_len+1);

//transfer valid characters from raw buffer

for (i=0, j=0; i < input_len; i++) {
if (valid_char (input_buffer [i])) {

sequence [j++] = input_buffer [i]; }

}
sequence [seq_len] = ;

//allocate int array for all the positions

valid_cpg_positions = (int*) malloc (seq_len *sizeof(int));

for (i=0; i<seq_len; i++) valid_cpg_positions[i] = 0;

/* YOUR CpG ISLANDS DISCOVERY COD E HERE */

return 0; }