[Bioperl-l] retrieval of PRELIMINARY uniprot sequences using Bio::Registry fails

Brian Osborne osborne1 at optonline.net
Sat Sep 2 16:17:34 EDT 2006


Bug, presumably in SeqIO/swiss.pm. Can you send me a small file with such a

Brian O.

On 9/1/06 6:11 AM, "Daniel Lang" <daniel.lang at biologie.uni-freiburg.de>

> Hi,
> when using Bio::Registry (bioperl-live) to fetch uniprot entries from
> local indexed uniprot *.dats, I had to realize that several entries
> could not be retrieved despite the fact that they are present in the
> files! A closer look reveals that they are of status PRELIMINARY:
> uniprot_trembl.dat:ID   Q16EZ1_AEDAE   PRELIMINARY;   PRT;   222 AA.
> I don't "grep" PRELIMINARY anywhere in my cvs checkout..
> I also can't retrieve the sequences from the online database defined as
> follows:
> [swissprot_ebi]
> protocol=biofetch
> location=http://www.ebi.ac.uk/cgi-bin/dbfetch
> dbname=swall
> Is this a bug or a feature? If its a feature, how can I bypass it?
> Thanks in advance,
> Daniel

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