[Bioperl-l] reading ace files

[Brian Osborne]

Susan,

I just installed the latest AcePerl (1.83) from CPAN and the following
worked:

use Bio::SeqIO;
$in = Bio::SeqIO->new( -file => "t/data/test.ace" );
$obj = $in->next_seq;
print $obj->seq;

MVN etc.


But I can't speak to the specific example you're describing, when the file
is phrap output. But Ace format is so straightforward, I wouldn't think that
phrap's output is not real Ace format....

Brian O.


-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Susan J. Miller
Sent: Friday, May 24, 2002 12:39 PM
To: bioperl
Subject: [Bioperl-l] reading ace files

Can bioperl read ace files such as those produced by phrap?  I tried
this using the SeqIO module but next_seq and next_primary_seq both
return null on my file:

 $in = Bio::SeqIO->new('-file' => $fil, '-format' => 'ace', 'dna' =>
'dna');
 while ($seq = $in->next_seq()) {
        print "seq $seq\n";
        print "SeqID $seq->id $seq->subseq(1,10) \n";
 }


--
Thanks,
-susan

Susan J. Miller
Biotechnology Computing Facility
Arizona Research Laboratories
Bio West 228
University of Arizona
Tucson, AZ  85721
(520) 626-2597
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