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making a list of sequences in fasta_format

Tony van Kampen A.J.A.van.Kampen at freeler.nl
Thu Aug 22 03:06:53 EST 2002


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:


use strict;
use warnings;
use Ace;

my $dblocation = "/home/aerts/docs/chickace/chickace";

my $db = Ace->connect(-path => "$dblocation") || die "Could not open

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


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
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The Netherlands

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