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Re: text file problem

by hipowls (Curate)
on May 10, 2008 at 21:02 UTC ( #685909=note: print w/replies, xml ) Need Help??

in reply to text file problem

I think your problem is

  • you have a large file
  • you have created a new file with line endings removed
  • now you want to read in characters between two positions in the new file
To do that you can use sysseek and sysread.
use Fcntl qw(SEEK_SET); my $input = '...'; my $start = 1_490_117; my $end = 1_492_312; my $length = $end - $start +1; open my $fh, '<', $input or die "Can't open $input: $!"; sysseek($fh, $start, SEEK_SET) or die "Can't seek to $start in $input: + $!"; my $sequence; my $read = sysread $fh, $sequence, $length; die "Failed to read $length bytes from $input, got $read" if $length != $read;
Now $sequence will contain the DNA sequence from 1,490,117 to 1,492,312 including both end points.

Note: sysread and sysseek use unbuffered IO, don't mix calls to them on a filehandle using other functions such as read, <> or eof.

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[LanX]: yep
[erix]: or Ctrl-U to view current html :P
[LanX]: name not id
[LanX]: id isn't approved AFAIK
[LanX]: name works
erix feels silly for having actually tested that contiguous values make no difference in CLUSTERing a table (At least, in postges)
[LanX]: Perl Monks Approved HTML tags
[LanX]: erix and his postguess ...
[erix]: (Grrres...)
[dabella12]: I have a problem install tK on CeontOs using perl 5.24

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