[Bioperl-guts-l] [Bug 3095] seq_version() in Bio::PrimarySeq not found

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Jul 16 17:29:08 EDT 2010


------- Comment #3 from cjfields at bioperl.org  2010-07-16 17:29 EST -------
The consensus on this is that version() and seq_version() can be two different
things; version() corresponds to any sequence version (local, remote,
whatever), whereas seq_version() corresponds to the sequence database version
(e.g. what one gets from a seq record).  

Saying that, I've noticed several inconsistencies with how the two are used. 
For instance, SeqIO::genbank and SeqIO::embl use seq_version (which seems
correct), whereas SeqIO::swiss uses vanilla PrimarySeq::version().  In cases
such as this, I suggest we always set seq_version() for sequence record
versions via SeqIO, then have seq_version() fall back to returning version()
unless explicitly set.  This should catch issues with legacy cases like
SeqIO::swiss being the odd one out.

If I don't see much objection, I'll implement the latter behavior on a branch.  

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