[Bioperl-l] Unusual behaviour of SeqIO::tigr

Morten Lindow morten at binf.ku.dk
Thu Mar 4 10:57:11 EST 2004

I am trying to build a table of genomic features from the tigrxml-format 
of a rice (pseudo)chromosome.

However the tigr-parser seem to behave differently from genbank/embl: 
tigr.pm considers every TU/etc an  individual sequence, and hence resets 
its coordinate system every time it starts on a new TU.

My question is:
Is there a bioperl-way to get to the global coordinates, like when I am 
parsing a genbankfile of a whole chromosome?

my $tigrin = Bio::SeqIO->new( -format => 'tigr', -file => 'chr01.xml');

while (my $seq = $tigrin->next_seq){ #I would expect this loop to run 
only once
    foreach my $feat ( $seq->get_SeqFeatures ) {
        foreach my $location ($feat->location->each_Location){
                print $location->to_FTstring, "\n";


More information about the Bioperl-l mailing list