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Help with sort and keep data record to calculate N50 in c

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# 1  
Old 07-18-2011
Help with sort and keep data record to calculate N50 in c
Input_file_1
Code:
#content_1
A
#content_2
AF
#content_3
AAR
#content_4
ASEI
#content_5
AS
#content_6
ADFSFGS

Rules:
1. Based on c program to calculate content of each "#". Result getting from the above Input_file_1 are 1,2,3,4,2,7;
2. Sort length on reverse order (descending order). 7, 4, 3, 2, 2, 1, 1;
3. Hope that the program able to store the above record (7, 4, 3, 2, 2, 1, 1) temporary for downstream analysis;
4. Sum all the total of Input_file_1: 7 + 4 + 3 + 2 + 2 + 1 + 1 = 20;
5. Divide (50%) the total sum of Input_file_1 as a threhold value: 20/2 = 10;
6. N50 must be equal to or greater than 50% of the total sum in Input_file_1 (10);
7. 7+4 = 11 (greater than 10);
Desired output result after running c program:
Code:
4

Many thanks for any advice.
# 2  
Old 07-18-2011
I don't understand step 7. why is output 4? I googled N50, it typically means how many of the largest integers need to be added together to equal 50%, so 7+4=11, requires 2 integers and output is 2? I guess you want the smallest member.

I think this is proper solution, finally. Using your example file:

Code:
[mute@geek ~/test]$ ./n50 n50.txt
4

Code:
#include <stdio.h>
#include <string.h>
#include <stdlib.h>

#define MAXLINES        32768

int lines[MAXLINES];
int line_count = 0;

int qsort_cmp(const void *p1, const void *p2)
{
        return (*(int *)p2 - *(int *)p1);
}

int main(int argc, char**argv)
{
        FILE *fh;
        char buf[512];
        int i, sum = 0, threshold;

        if (argc != 2)
        {
                printf("Usage: %s <input file>\n", argv[0]);
                return -1;
        }

        if ((fh = fopen(argv[1], "r")) == NULL)
        {
                perror("fopen");
                return -1;
        }

        while (fgets(buf, sizeof(buf), fh))
        {
                int len = strlen(buf);

                /* skip comments */
                if (buf[0] == '#') continue;

                /* strip newline at end */
                buf[--len] = 0;

                /* add to sum. */
                sum += len;

                /* keep record */
                lines[line_count++] = len;
        }

        qsort(lines, line_count, sizeof(int), qsort_cmp);

        threshold = sum / 2;

        for (i = sum = 0; (sum += lines[i]) < threshold; i++)
                ;

        printf("%d\n", lines[i]);

        return 0;
}

Last edited by neutronscott; 07-18-2011 at 02:28 AM.. Reason: had it totally wrong at first
This User Gave Thanks to neutronscott For This Post:
cpp_beginner
# 3  
Old 07-18-2011
Hi, friend.
This is one of the thread that mention well about N50 calculation, Calculating an N50 from Velvet output | (R news & tutorials)
The N50 of my example should be 4 instead of 2.
I'm trying with your approaches now with test file.
Hopefully we getting the same approaches Smilie
# 4  
Old 07-18-2011
As per your PM, the content should handle newlines. Also, I added DEBUG statements so you can view what the program is doing...

Code:
#include <stdio.h>
#include <string.h>
#include <stdlib.h>

#define DEBUG
#define MAXLINES        32768


int lines[MAXLINES];
int line_count = 0;

int qsort_cmp(const void *p1, const void *p2)
{
        return (*(int *)p2 - *(int *)p1);
}

int main(int argc, char**argv)
{
        FILE *fh;
        char buf[512];
#ifdef  DEBUG
        char contentblock[512];
#endif
        int i, sum = 0, threshold;

        if (argc != 2)
        {
                printf("Usage: %s <input file>\n", argv[0]);
                return -1;
        }

        if ((fh = fopen(argv[1], "r")) == NULL)
        {
                perror("fopen");
                return -1;
        }

#ifdef  DEBUG
        /* if a block is given before first '#' ... */
        strcpy(contentblock, "null");
#endif
        lines[0] = 0;
        while (fgets(buf, sizeof(buf), fh))
        {
                int len = strlen(buf);
                /* strip newline at end */
                buf[--len] = 0;
                /* new content block */
                if (buf[0] == '#') {
#ifdef  DEBUG
                        printf("%s length %d\n", contentblock, lines[line_count]);
                        strcpy(contentblock, buf + 1);
#endif
                        lines[++line_count] = 0;
                        continue;
                }
                /* keep record */
                lines[line_count] += len;
                /* add to sum. */
                sum += len;
        }
        threshold = sum / 2;
#ifdef  DEBUG
        printf("%s length %d\n", contentblock, lines[line_count]);
        printf("sum = %d, threshold = %d\n", sum, threshold);
        printf("Before sort: ");
        for (i = 0; i <= line_count; i++)
                printf("%d%s", lines[i], (i == line_count) ? "\n" : " + ");
#endif

        qsort(lines, line_count + 1, sizeof(int), qsort_cmp);
#ifdef  DEBUG
        printf("After sort: ");
        for (i = 0; i <= line_count; i++)
                printf("%d%s", lines[i], (i == line_count) ? "\n" : " + ");
#endif
        for (i = sum = 0; (sum += lines[i]) < threshold; i++)
        {
#ifdef  DEBUG
                printf("%d%s", lines[i], (sum >= threshold) ? "\n" : " + ");
#endif
        }

        printf("%d\n", lines[i]);

        return 0;
}

This User Gave Thanks to neutronscott For This Post:
cpp_beginner
# 5  
Old 07-19-2011
Many thanks, neutronscott.
Your program work very fast for huge data Smilie
It is amazing.
Do you have any idea how to edit the program to allow it print out only the N50 number instead of whole data analysis detail?
I try to edit it.
But can't work Smilie
Thanks for your assist.
# 6  
Old 07-19-2011
#undef DEBUG
This User Gave Thanks to neutronscott For This Post:
cpp_beginner
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