Re: Extracting DNA sequences from FASTA files

to reverse the bases:

my %ibase;
$ibase{"A"} = "T";
$ibase{"T"} = "A";
$ibase{"C"} = "G";
$ibase{"G"} = "C";
$ibase{"N"} = "N";
sub seq_inverse
{
    my ($nseq) = @_;
    my @seq = split(m//,$nseq);
    my $lim = @seq;
    my $inv = "";

    $inv .= $ibase{$seq[$lim]} while($lim > 0 and $lim--);

    return $inv;
}
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Comment on Re: Extracting DNA sequences from FASTA files Download Code

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Re^2: Extracting DNA sequences from FASTA files by educated_foo (Vicar) on Jun 29, 2009 at 15:36 UTC
It's easier when you work with Perl rather than against it: `sub reverse_complement { local $_ = shift; y/ACGT/TGCA/; reverse; }` [download] As for the OP's question, FASTA is a pretty simple format other than the various stuff people put in the sequence labels. So your code will probably look something like this: `while (<FASTA>) { chomp; if (/^>\s(.)/) { # it's a sequence label $name = $1; } else { # it's sequence data } }` [download]	[reply] [d/l] [select]

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Re^2: Extracting DNA sequences from FASTA files
by educated_foo (Vicar) on Jun 29, 2009 at 15:36 UTC

sub reverse_complement {
    local $_ = shift;
    y/ACGT/TGCA/;
    reverse;
}
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while (<FASTA>) {
    chomp;
    if (/^>\s*(.*)/) {
        # it's a sequence label
        $name = $1;
    } else {
        # it's sequence data
    }
}
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