[Bioperl-l] How to proceed with 1.4?

[Ewan Birney]

On Tue, 9 Dec 2003, Heikki Lehvaslaiho wrote:

> 
> I have so far relased three snapshots from the bioperl core/live cvs head. 
> Things have settled down a bit, but there are still outstanding issues. 
> Especially:
> 
> - restriction analysis fixes need to merged and commited (Rob)
> - SearchIO::psiblast & related module removal (Steve)
> - really long qualifier names in sequence feature tables (Ewan?) #1561
> 


Ok... This is now "fixed" to behave in the same way as the EMBL feature 
dumping here at EBI does. A little detour here:


   - The feature table document just has a line limit on it. It does not 
specify how to break words up across lines in particular in "continuation"
mode

   - @EBI the suggestion (implemented in the bioperl code) is that one
breaks at hypens and commas as well as spaces

   - This causes a round-tripping problem because the break will get 
interpreted as a white space.


This round tripping problem is present now in the GenBank/EMBL system
anyway, so... I've just made Bioperl work the same way ;).


Proof:


ID   id         standard; DNA; UNK; 27 BP.
XX
AC   unknown;
XX
DE   
XX
FH   Key             Location/Qualifiers
FH
FT   CDS             1..2
FT                   /product="this-is-a-really-long-silly-name-which-goes-aaay-
FT                   too-long-and-makes-life-difficult"
FT                   /product2="N-acetylglucosaminyl-
FT                   phosphatidylinositolbiosyntheticprotein, putative"
XX
SQ   Sequence 27 BP; 11 A; 0 C; 6 G; 10 T; 0 other;
     atggttagaa attttgaaat tgaaatg                                            
27
//




I also have some tests failing on my installation, which is linux,

[birney at localhost bioperl-live]$ perl -v

This is perl, v5.6.0 built for i386-linux

Copyright 1987-2000, Larry Wall




Failed Test  Status Wstat Total Fail  Failed  List of failed
-------------------------------------------------------------------------------
t/BioDBGFF.t      0   139   133    4   3.01%  130-133
t/Coalescent.t  255 65280    11   10  90.91%  2-11
t/GFF.t         255 65280    32   12  37.50%  21-32
t/GuessSeqForma              44    1   2.27%  9
t/RestrictionAn             111    9   8.11%  80, 82, 85, 98-99, 101-104
t/RestrictionIO              14    2  14.29%  4, 10
t/RootI.t         2   512    10    3  30.00%  8-10
t/tutorial.t      2   512    21    3  14.29%  19-21





Not sure how many of these you know about Heikki - I tend not to have XML 
things installed, so that triggered some game stuff in some somewhere...