[Bioperl-l] SeqIO::swiss.pm

[Hilmar Lapp]

Even though the swissprot parser has improved a lot thanks to Lorenz and
others (maybe even myself ;) there are still some flaws in output, among
them being e.g.

1) superfluous empty line after the seq (does this hurt according to the
specs?)
2) empty GN line (again, does this hurt?)
3) truncation of the OS line (at least in some cases)
4) OC line not being written correctly (at least in some cases)

An example is accession P25222 (SwissProt) (mentioned in bug report
#168). I can provide the entry if you need it.

Any volunteers for fixing those things? Lorenz, still enthusiastic?

The version present in the branch-06 seems to be more or less broken, at
least with respect to output printing. The question is whether or not we
can take over the version from main trunk. Lorenz, could you summarize
the modules you had to fix or even add in order to get the parser work?

I'm afraid this can break the scope of a bugfix-only. If so, replace at
least write_seq on the branch with throwing an exception? Would be fair
to people who assume that the result is at least half-way ok (it's not).

	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
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