fgarret at ub.edu
Mon Sep 18 10:48:40 EDT 2006
When trying to fetch some GFF features from a GFF DB there are some
options that do not seem to be working well.
In Flybase, on the - strand features, the start is bigger than the stop
positions (they assume the start of the feature rather than the start of
I managed to fix it by using the '$db->absolute(1)'. However, when
performing a '$segment->refseq($segment);' (to reset the positions) the
absolute option is ignored and returns to "Flybase style" positions.
Here's the code I'm using
# Open the sequence database
my $db = Bio::DB::GFF->new(-adaptor => 'dbi::mysql',
-dsn => 'dbi:mysql:dmel_gff:123.456.78.90',
-user => 'user',
-pass => 'pass') || die("database open failed");
my $segment = $db->segment(-name => '4', -start => 20000, -end => 25000);
my @features = $segment->features(-types => ['gene', 'exon', 'intron',
'five_prime_UTR', 'three_prime_UTR', 'CDS']) or die "no features";
my $gffio = Bio::Tools::GFF->new(-file => '>'.'gff.out.gff',
-gff_version => 3);
Does anyone knows what can be going wrong?
Thanks in adv,
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