Desired Output Archives - Bartle Doo Article Archives

By yifangt

Sounds like a homework, but not! This is only for self study. I know the better way would be in perl which is too slow if the file is too big (normally ~15GB), but I am trying to pick up C said to be more faster and use less memory. Can someone help me with my code? Here’s the file (which is a typical fastq format—mean every four lines as a unit): infile.txt

Code:

@Mseq1

AGCTG

+

XX%%A

@Mseq2

AGCGG

-

&X#%A

@Mseq3

AGCCG

+

#X%#A

Desired Output: outfile.txt

Code:

@Mseq1 AGCTG + XX%%A

@Mseq2 AGCGG - &X#%A

@Mseq3 AGCCG + #X%#A

Code:

#include 

#include 

#include 
struct node

{

  char readName[251];

  char readSeq[251];

  char strand;

  char readQual[251];

  struct node *next;

};
int main ()

{

  FILE *fp;

  int count;

  char *line;

  count = 1;

  char filename[30] = "infile.txt";

  struct node *read, *pre, *p;

  struct node *first = NULL;
  fp = fopen (filename, "r");
  while (fgets (line, sizeof (line), fp) != NULL)    /* read a line */

    {

      read = (struct node *) malloc (sizeof (struct node));

      while (count % 4 == 1)

    {

      strcpy (read->readName, line);

    }

      count++;

      while (count % 4 == 2)

    {

      strcpy (read->readSeq, line);

    }

      count++;

      while (count % 4 == 3)

    {

      strcpy (read->strand, line);

    }

      count++;

      while (count % 4 == 0)

    {

      strcpy (read->readQual, line);

    }

      count++;

      read->next = NULL;

      pre = p = first;
      while (p != NULL)

    {

      pre = p;

      p = p->next;

    }

      if (pre != NULL)

    pre->next = read;

      else

    first = read;
      fclose (fp);
      ...read more 
Source: FULL ARTICLE at The UNIX and Linux Forums

By DerSeb

Hello all,

I would like to output a random number within a range for every line using awk and shuf. I think I’m almost there, but I don’t know how to pass arguments to shuf within my awk script:

Input

Code:

1 12190 12227

1 12595 12721

1 13403 13639

1 14362 14829

1 14970 15038

awk:

Code:

awk '{ a = (shuf -i $2"-"$3 -n 1)}{print $1,a}' Input

Desired Output (with second column being a random number between field 2 and 3 of input file):

Code:

Al I get so far is

Code:

1 012190-122271

1 012595-127211

1 013403-136391

1 014362-148291

1 014970-150381

Any help would be greatly appreciated!

Seb

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Read sequence file into linked list in C.

Using and passing arguments to shuf within awk

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