Bioperl: SwissProt parser (Bio::SeqIO::swiss.pm)

[Hilmar Lapp]

Dear all,

the SwissProt parser appears to be completely broken. Not only was indeed
feature table parsing and writing missing, it would even miss lines from
references and other sections due to bugs in the record looping code. Even
worse, it would under certain conditions (which are not so infrequent - I
found it about every 20 entries) overread the entry boundary and thereby lose
complete entries. Note that this happens silently, you wouldn't notice. I hope
that no-one used this parser so far for serious work.

I've now done the following things:
1) Added code to parse the feature table. So far it seems to work, SwissProt
is completely through without obvious errors, but TrEMBL isn't yet (I have
only a single CPU machine at home). No feature table writing yet, and someone
else should volunteer for this.
2) Fixed the code looping over the lines of an entry. Seems to work now as
well, entries are no longer lost. DB-references and other sections should be
complete now.
3) Other smaller fixes (like methods unnecessarily duplicated from the base
class SeqIO).
4) A small further fix to FTHelper.pm to make it aware that either start or
end of a feature may be unknown, in which case the respective end won't be
set. (So, theoretically, the feature object should return undef when queries
for this end, but I haven't tested.)

Note that I'm talking about the main trunk. I leave it up to James to
propagate the fixes to the branch as he sees fit. IMHO just copying the files
should be safe.

Cheers,

	Hilmar

-- 
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Hilmar Lapp                                      email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics                   phone: +43 1 86634 631
A-1235 Vienna                                      fax: +43 1 86634 727
ROI: Bioinformatics (arrays, expression, seqs), Programming, Databases,
     Mountain Biking (hard tail, hard fork: feel the trail)
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