making a list of sequences in fasta_format

Keith Bradnam krb at sanger.ac.uk
Wed Aug 28 03:56:45 EST 2002


Hi Tony,

Have you tried using the asDNA function of Aceperl?

The following works for me in extracting all DNA sequences from a group of
sequences:

#!/usr/local/bin/perl5.6.1 -w

use Ace;

$db = Ace->connect(-path  =>  '/wormsrv2/current_DB') || die "Can't
connect\n";

my @seqs = $db->fetch(Sequence => "AH6.*");

foreach $seq (@seqs){
    $fasta_seq = $seq->asDNA();
    print "$fasta_seq\n";       
}  
   

Hope this helps.

Keith



On 22 Aug 2002, Tony van Kampen wrote:

> ls,
> 
> I encountered the following problem:
> 
> I know how to export a single DNA_sequence in fasta format, but now 
> would like to do it batch_wise.
> 
> The problem seems to be that ?DNA is a class of the "A"_type.......
> 
> I tried with aceperl this:
> 
> start of code:
> 
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> use Ace;
> 
> 
> my $dblocation = "/home/aerts/docs/chickace/chickace";
> 
> my $db = Ace->connect(-path => "$dblocation") || die "Could not open
> connection\n";
> 
> my @sequences = $db->fetch("Sequence");
> 
> foreach my $seq (@sequences) {
> ## Om een lijst te krijgen van alle tags die aan het DNA object hangen.
>    my @more_tags = $seq->at('DNA')->tags;
>    foreach (@more_tags) { print $_, "\n" }
> 
> ## Om de eigenlijke FASTA file aan te maken.
> #   if ($seq->DNA) { print ">", $seq, "\n", $seq->DNA, "\n" }
> 
> }
> 
> 
> print Ace->error;
> print $db->error;
> 
> end of code
> 
> The reply is:
> 
>    Can't call method "tags" on an undefined value at
>         ./GetSequencesFromChickace.pl line 15, <GEN0> line 1.
> 
> I also tried tablemaker but then also the acces to a tag in ?DNA is 
> denied: youn cannot select a tag in non-B-class: DNA
> 
> 
> 
> Is there a solution?
> 
> I'm using Linux Acedb4.9j
> 
> cheers,
> 
> Tony
> -- 
> Tony van Kampen
> Bio-informatics specialist
> Wageningen University Animal Sciences
> The Animal Breeding and Genetics group
> 
> E-mail: Tony.VanKampen at alg.vf.wau.nl
> 	A.J.A.van.Kampen at freeler.nl
> 	
> Telephone: 	+31 317 483049 (work)
> 		+31 6 12052457 (mobile)
> 		+31 026 4426058 (home)
> 		
> Telefax: +31 317 483929
> 
> P.O. Box 338
> 6700 AH Wageningen
> The Netherlands
> 
> Visiting address:
> Zodiac, Marijkeweg 40
> 6709 PG Wageningen
> The Netherlands
> 
> 

~  Keith Bradnam - WormBase group: http://www.wormbase.org/
~ 
~  The Wellcome Trust Sanger Institute,
~  Hinxton, Cambridge, CB10 1SA, UK.  Tel: 01223 494922






More information about the Acedb mailing list