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
