[Bioperl-l] DB::GFF

[Lincoln Stein]

If you use refseq() to set relative addresses, then you must be prepared to
have start features that are greater than end features. This is so that the
identity of a coordinate doesn't change depending on the direction you are
looking in!

Lincoln

On 9/18/06, Filipe Garrett <fgarret at ub.edu> wrote:
>
> Hi all,
>
> 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
> the sequence).
>
> 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
>
> 'use Bio::DB::GFF;
> use Bio::Tools::GFF;
>
> # 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");
>
> $db->absolute(1);
> my $segment = $db->segment(-name => '4', -start => 20000, -end => 25000);
> $segment->refseq($segment);
> my @features = $segment->features(-types => ['gene', 'exon', 'intron',
> 'five_prime_UTR', 'three_prime_UTR', 'CDS']) or die "no features";
> print(scalar(@features)."\n");
>
> my $gffio = Bio::Tools::GFF->new(-file => '>'.'gff.out.gff',
> -gff_version => 3);
> $gffio->write_feature(@features);
>
> exit(1);'
>
>
> Does anyone knows what can be going wrong?
>
> Thanks in adv,
> FG
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-- 
Lincoln D. Stein
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