Re^4: Converting Filehandle to Array call in Object Creation

The handle used by Bio::AlignIO (when 'fasta' is specified) must return ">Seq1\n", "AAAAAAAAAAAAAAA\n", ">Seq2\n", "AAAAAAAGGAAACCA\n" on subsequent calls to a read line, but yours returns "AAAAAAAAAAAAAAA" and "AAAAAAAGGAAACCA".

I suppose you could change:

my $fh = Tie::Handle::FromArray->new(\@array);
[download]

my $fh = Tie::Handle::FromArray->new([
   map { ">Seq".$seq_id++."\n", "$_\n" } @array
]);
[download]

but it would be nice if the tied class did that for you instead of creating a new array twice the size of the original one.

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Re^5: Converting Filehandle to Array call in Object Creation by holli (Abbot) on Apr 27, 2005 at 19:03 UTC
Patch: use the last element of the array for a counter. `sub TIEHANDLE($;$) { my $pkg = shift; my $ref = shift \|\| []; push @{$ref}, 0; bless( $ref, $pkg ); } sub READLINE { my $ref = shift; return @{$ref} > 1 ? ">Seq" . ++$ref->[-1] . "\n" . shift (@{$ref} +) . "\n" : undef; }` [download] so `use Tie::Handle::FromArray; my $fh = new Tie::Handle::FromArray ( ["AAAAAAAAAAAAAAA", "AAAAAAAGGAA +ACCA"] ); while (<$fh>) { print; }` [download] prints `>Seq1 AAAAAAAAAAAAAAA >Seq2 AAAAAAAGGAAACCA` [download] holli, /regexed monk/	[reply] [d/l] [select]

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Re^5: Converting Filehandle to Array call in Object Creation
by holli (Abbot) on Apr 27, 2005 at 19:03 UTC

sub TIEHANDLE($;$) 
{
    my $pkg = shift;
    my $ref = shift || [];
    push @{$ref}, 0;

    bless( $ref, $pkg );
}

sub READLINE 
{
    my $ref = shift;
    return @{$ref} > 1 ? ">Seq" . ++$ref->[-1] . "\n" . shift (@{$ref}
+) . "\n" : undef;
}
[download]

use Tie::Handle::FromArray;

my $fh = new Tie::Handle::FromArray ( ["AAAAAAAAAAAAAAA", "AAAAAAAGGAA
+ACCA"] );
while (<$fh>) { print; }
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>Seq1
AAAAAAAAAAAAAAA
>Seq2
AAAAAAAGGAAACCA
[download]

holli, /regexed monk/

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