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.nlA.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