[Bioperl-l] Bio::SeqIO::fasta id printing

[Jason Stajich]

[ Warning: Boring bioperl sequence objects internals ]

Bio::SeqIO::fasta prints a sequence using $seq->id() which is mapped to
display_id in bioperl.  However in ensembl, which uses the PrimarySeqI.pm
model, they have an id() method which refers to their internal id for the
sequence object.  I would propose we change Bio::SeqIO::fasta to print
the id with $seq->display_id() unless there is a fundamental reason for
using the id() call in fasta.pm.

In looking at these methods I'm also confused why there is implementation
in PrimarySeqI and PrimarySeq for the id() method since it is just
aliased to display_id in both modules.  

References:
  Bio::SeqIO::fasta.pm v1.23 line:168
  Bio::PrimarySeqI v1.29 line 629
  Bio::Seq.pm v1.38 line 480


Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/