This is a fasta-formatted sequence file, right? You're best bet for doing this is might be the BioPerl library. They have both a regular fasta-parser as well as a special indexed parser for genome-sized files. The latter works really well if you need to get subsequences from a file. For instance, I use the indexed-version when I want to extract all mRNA sequences from a single chromosome.

Here is the code for using the indexed-version. It processes every mRNA on every chromosome in a typical eukaryotic genome in about 30 minutes on a P4.

# set up chromosome sequence object
my $file = $chromosome.'.fa';
my $seqio = Bio::SeqIO->new(
    -format    => 'largefasta',
    -file    => $file
    );

# set up range parameters
my $strand = '+';
my $seq_start = 1_000_000;
my $seq_end   = 2_000_000;
my $downstream= 10_000;

# handle sequences on both strands
if ($strand eq '+') {
    $seq_start = $tx_start - $upstream;
    $seq_end   = $tx_start + $downstream;
    if ($seq_start < 0) { next(); }
    if ($seq_end > $length) { next(); }
    $seq_mRNA  = $seq_chr->trunc($seq_start,$seq_end);
    }
elsif ($strand eq '-') {
    $seq_start = $tx_end + $upstream;
    $seq_end   = $tx_end - $downstream;
    if ($seq_end < 0) { next(); }
    if ($seq_start > $length) { next(); }
    $seq_mRNA  = $seq_chr->trunc($seq_end,$seq_start)->revcom();
    }
else {
    warn "No strand: $strand!\n";
    next();
    }

# write seq to a file
my $outfile = $mRNA.'.fasta';
open(OUT, '>', $outfile);
print OUT ">$mRNA\n", $seq_mRNA->seq();
close(OUT);

[download]

And there are always the usual caveats with BioPerl -- great user support group, fairly big initial learning curve, highly object-oriented library....

-Tats

In reply to Re: character-by-character in a huge file by Itatsumaki
in thread character-by-character in a huge file by mushnik

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.