[Bioperl-l] retrieving sequences by ID

[Jason Stajich]

Bio::DB::Fasta and Bio::Index::Fasta both do this for you.  You might 
need to provide your own ID parsing header if you only want the bit 
before the '|' be part of the id.
These modules build a persistent index so they remove the need to 
re-read the file on each run of your application.

http://bioperl.org/HOWTOs/Beginners/indexing.html
-jason
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

On Apr 27, 2005, at 10:33 AM, Sean O'Keeffe wrote:

> Hi all,
> This is probably an easy problem for ye, but one I'm having difficulty
> with none the
> less.
> I'm trying to extract only sequences from a fasta file (containing
> ~38,000 sequences)
> containing a specific ID in the header line e.g.
> return only the sequence for header containing 'ABCD12346' from:
>> ABCD12345|followed by the rest of the description
> acgtacgtgttttgggccctttaaa.....
>> ABCD12346|description
> acgtacgtgttttgggccctttaaa.....
>> ABCD12347|description
> acgtacgtgttttgggccctttaaa.....
> ...
>
> The specific ID's are contained in a list(~20,000) which I want to 
> loop through.
> This is what I have done so far w/out any luck:
>
> ############################
>
> use strict;
> use lib "/usr/lib/perl5/site_perl/5.8.1/";
> use Bio::SeqIO;
>
> my (@ids)=@_
> my $seq_in = Bio::SeqIO->new( '-format' => "fasta",
>                               '-file' => "$fastafile");
> my $seq_out = Bio::SeqIO->new( '-format' => "fasta",
>                               '-file' => "$outfile");
> for ($i=0;$i<=scalar(@ids);$i++){
> while ($sequence = $seq_in->next_seq){
>         if ($sequence->display_id =~ /^>$ids[$i](.*$)/){
>                 $seq_out->write_seq($sequence);
>         }
> }
> }
> exit;
>
> #############################
>
> This has so far returned a list of 3 fasta headers and the programs
> then finishes without errors.
> I'd like to know where I'm going wrong and if possible, how I could
> improve on things to prevent memory usage/speed it up.
>
> Thanks in advance,
> Sean O'Keeffe.
>
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