Re: Converting Filehandle to Array call in Object Creation

You can do that by using a tied Filehandle. Create this module:

package Tie::Handle::FromArray;

use strict;
use warnings;

sub new 
{
    my $pkg = shift;
    my $handle = \do {local *HANDLE};
    
    tie *{$handle}, $pkg, @_; 
    
    return $handle;
}



sub TIEHANDLE($;$) 
{
    my $pkg = shift;
    my $ref = shift || [];

    bless( $ref, $pkg );
}

sub READLINE 
{
    return shift @{+shift}
}

"this is a false statement.";
[download]

and alter your script:

my $fh = Tie::Handle::FromArray->new( ["AAAAAAAAAAAAAAA", "AAAAAAAGGAA
+ACCA"] );
my $in  = Bio::AlignIO->new(-fh => $fh, -format => 'fasta');
[download]

holli, /regexed monk/

Comment on Re: Converting Filehandle to Array call in Object Creation Select or Download Code

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Re^2: Converting Filehandle to Array call in Object Creation by ikegami (Patriarch) on Apr 15, 2005 at 14:23 UTC
Your tied class doesn't add ">Seq1", ">Seq2", etc to the stream. From what I saw, leaving those out causes the whole array to be treated as a single sequence (namely "AAAAAAAAAAAAAAAAAAAAAAGGAAACCA").	[reply]
Re^3: Converting Filehandle to Array call in Object Creation by holli (Abbot) on Apr 15, 2005 at 20:08 UTC
I must admit I don't get what you're saying. `use strict; use warnings; use Tie::Handle::FromArray; my $fh = new Tie::Handle::FromArray ( ["a","b"] ); while (<$fh>) { print "$_"; }` [download] prints `ab` [download] just as i would expect. can you clarify? holli, /regexed monk/*	[reply] [d/l] [select]
Re^4: Converting Filehandle to Array call in Object Creation by ikegami (Patriarch) on Apr 16, 2005 at 00:10 UTC
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] to `my $fh = Tie::Handle::FromArray->new([ map { ">Seq".$seq_id++."\n", "$_\n" } @array ]);` [download] but it would be nice if the tied class did that for you instead of creating a new array twice the size of the original one.	[reply] [d/l] [select]
Re^5: Converting Filehandle to Array call in Object Creation by holli (Abbot) on Apr 27, 2005 at 19:03 UTC
Re^4: Converting Filehandle to Array call in Object Creation by tlm (Prior) on Apr 16, 2005 at 00:33 UTC
What ikegami is referring to, I believe, is that the method is expecting a file in FASTA format, which means that sequences are always preceded by a "description line" having the format `>foo bar baz and whatever else` [download] This line holds identifying info for the following sequence. Therefore, your tied array class would have to prepend to each array element some surrogate for this line (e.g. at minimum `">\n"`, or something more informative, such as `">$n\n"`, where `$n` is a class variable holding the current position in the input array). Another complication is that the FASTA format requires that all lines be at most 80 characters long. So your `READLINE` method would have to do a bit more processing and bookkeeping than simply spitting out the next array element. No biggie. Alternatively, the module in question may be able to handle some other file format that is more easily mimicked with a tied array than FASTA is. the lowliest monk	[reply] [d/l] [select]