How to "jump" to a line of a file, rather than read file line by line, using Perl - perl

Question

I am opening a file containing a single but very long column. I want to retrieve from it just a short segment, starting at a specified line and ending at another specified line. Currently, my script is reading the file line by line until the desired lines are found. I am using:
my ( $from, $to ) = ( some line number, some larger line number );
my $count = 1;
my #seq = ();
while ( <SEQUENCE> ) {
print "$_ for $count\n";
$count++;
while ( $count >= $from && $count <= $to ) {
push( #seq, $_ );
last;
}
}
print "seq is: #seq\n";
Input looks like:
A
G
T
C
A
G
T
C
.
.
.
How might I "jump" to where I want to be?

Answer 1

You'll need to use seek to move to the correct portion of the file. ref: http://perldoc.perl.org/functions/seek.html
This works on bytes, not on lines, so generally if you need to use line seeking its not an option. However, since you're working on a fixed length line (2 or 3 bytes depending on your platform's EOL encoding) you can multiply the line length by the line you want (0 indexed) and you'll be at the correct location for reading.

Answer 2

If you happen to know that all the lines are of exactly the same length (accounting for line ending characters, generally 1 byte on Unix/Linux and 2 on Windows), you can use seek to go directly to a specified point in the file
The seek function lets you specify a file position in bytes/characters, not in lines. In the general case, the only way to go to a specified line number is to read from the beginning and skip that many lines (minus one).
Unless you have an index mapping line numbers to byte offsets; then you can look up the specified line number in the index and use seek to jump to that location. To do this, you have to build the index separately (a process that will require reading through the entire file) and make sure the index is always up to date. If the file changes frequently, this is likely to be impractical.
I'm not aware of any existing tools for building and using such an index, but I wouldn't be surprised if they exist. But it should be easy enough to roll your own.
But unless scanning the file to find the line number you want is a significant performance bottleneck, I wouldn't bother with the extra complexity.