The offset appears to make sense in the trimmed file. That is, excluding the spaces between the columns and the line numbers. Which suggests that Augustine might aviod slurping the file, by reading one line at a time (by leaving $/ unchanged) and windowing every input sequence (exon) (a sequence of lines which covers the exon).

You could also use `seek' and `sysread' (as suggested by Belgarion, but you'd have to work out an algorithm (quite simple I would guess) which converts the address within the trimmed file to the address within the formatted file. Something like... $address_in_file = $address_in_trimmed_file + $number_of_characters_for_line_numbering_for_first_line + ($address_in_trimmed_file / 10) + ($address_in_trimmed_file / 60) * ($one_character_for_new_line + $number_of_characters_for_line_numbering). Actually, I think that is a correct and yet unabusive way to solve this (every 10 characters you get a space, every 60 characters you get a new line and a line number).

On another note, though, I have experience with slurping large files, and can say that perl handles it pretty good. For example, I could semi-parse an 8Mb Xml file into an internal tree within seconds. I'm afraid I cannot say how substring handles large offset/length parameters, I thought it would work as expected.

In reply to Re^2: substr is behaving differently with small vs large strings by perldeveloper
in thread substr is behaving differently with small vs large strings by wadunn

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.