Thread: from perl to C

Dear all,
I am a newbie to C. I want to learn C very badly. i know the theory part of C, but i m not so good when it comes to writting real time programs in C. I m good at perl, but when i use the below program for a small file, it works fine. Not the same for a 10 gig file. So, i felt that writing the program in C would help. Please help me solve the problem, n also to learn C. Here is my problem.

I am comparing 2 files, i take information of left and right values from file 2, and extract numbers at the beginning(left value) and end(right value) of every string-numbers (based on their unique ID which starts with '>') from file 1.

Code:

file1:

>AAAT3R length=110
40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 
40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 38 38 38 40 40 39 40 
40 40 40 40 40 40 40 40 40 38 38 37 39 36 36 40 36 35 35 35 38 40 
35 35 33 35 35 35 40 40 40 40 37 37 38 38 38 40 40 40 40 40 40 40 
40 40 40 40 40 40 40 40 40 37 36 36 31 22 22 22 20 20 20 20 20 14
>AAA2OJ length=70
18 18 18 21 35 35 35 32 32 32 33 35 38 39 37 37 39 39 39 39 39 40 
40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 
40 39 39 37 35 35 39 37 37 37 37 37 37 37 37 37 37 33 32 32 30 20 
17 17 17 0

file2:

>AAAT3R_left length=6
TACATA
>AAAT3R_right length=62 ACTACTGATTTGATTATCTTTGATCTCTGTCGAACTAACTATATCTTAGTATGATCTTTAAT
>AAA2OJ_left length=14
TTTTGGACTATCTG
>AAA2OJ_right length=14
AGGCTGTTCTTTTN

result file(expected)

>AAAT3R_left length=6
40 40 40 40 40 40
>AAAT3R_right length=62
40 40 40 38 38 37 39 36 36 40 36 35 35 35 38 40 35 35 33 35 35 35 40 40
 40 40 37 37 38 38 38 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 37
 36 36 31 22 22 22 20 20 20 20 20 14 >AAA2OJ_left length=14
18 18 18 21 35 35 35 32 32 32 33 35 38 39
>AAA2OJ_right length=14
37 37 37 37 37 33 32 32 30 20 17 17 17 0
[download]

This is the code i have written so far, to get the desired output.

#!/usr/bin/perl -w
use strict;

our ($File1, $File2) = qw/file1 file2/;
open File1 or die "$File1: $!\n";
open File2 or die "$File2: $!\n";

my ($key, %results);
while (<File1>){
    next if /^\s*$/;
    chomp;
    if (/^>\s*(\S+)/){
        $key = $1;
    }
    else {
        $results{$key} = [ split ];
    }
}
close File1;

my ($len, $side, $str);
while (<File2>){
    next if /^\s*$/;
    if (/^>([^_]+)_(left|right).*?(\d+)\s*$/){
        print;
        $str = $1;
        $side = $2;
        $len = $3;
    }
    else {
        my @list;
        @list = @{$results{$str}};
        if ($side eq 'left'){
            die "$str is too short for a left slice of $len!\n"
            unless @list >= $len;
            print "@list[0..$len-1]\n";
        }
        else {
            die "$str is too short for a right slice of $len!\n"
            unless @list >= $len;
            print "@list[@list-$len..$#list]\n";
        }
    }
}
close File2;

Please help me do this in C.