[Bioperl-announce-l] bioperl 1.2.3 RC1

Steve Chervitz steve_chervitz at affymetrix.com
Wed Sep 17 05:04:29 EDT 2003

On Monday, Sep 15, 2003, at 10:05 US/Pacific, Jason Stajich wrote:
> Developers:
>  If you have any last minute changes - you need to get them in by 
> tomorrow
>  or let me know what you still have pending and I can hold up making a
>  final release.

I put in a small addition to SeqIO::fasta that allows you to specify 
which type of identifier to appear after the '>' in the generated fasta 
output (e.g., accession, accession.version, display, or primary). The 
new method is called preferred_id_type. This is only applicable to 
fasta format; other formats have special slots for different types of 
identifiers, so it didn't make sense to put this in SeqIO.pm. I also 
added a test for it in SeqIO.t.

Jason: Since this was such a trivial addition and doesn't affect 
existing functionality, I put in on the 1.2 branch as well as 
bioperl-live. However, since it is new functionality, I should have put 
it on the main trunk only. Let me know if you want to back it out of 
the branch.

One issue I haven't addressed is how to deal with SeqIO::MultiFile. 
This module should delegate any method calls it can't handle (such as 
preferred_id_type) to its current SeqIO object. This would also address 
other format-specific methods such as SeqIO::fasta::width().


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