[Bioperl-l] retrieval of PRELIMINARY uniprot sequences using Bio::Registry fails
cjfields at uiuc.edu
Wed Sep 6 14:59:01 UTC 2006
I have found the issue with Bio::SeqIO::swiss; apparently UniProt has
switched to using the following ID line format:
ID ENTRY_NAME DATA_CLASS; MOLECULE_TYPE; SEQUENCE_LENGTH.
For SwissProt ID's
ID CYC_BOVIN STANDARD; PRT; 104 AA.
ID GIA2_GIALA STANDARD; PRT; 296 AA.
For TrEMBL (preliminary protein):
ID Q5XPV6 PRELIMINARY; PRT; 231 AA.
SeqIO 'swiss' sequence output currently uses the first (SwissProt) version;
it's hardcoded in a sprintf() statement. I guess TrEMBL didn't have a
designation before, so this complicates things a little.
There are a few other (small) formatting differences I have also found which
we could update fairly easily.
In the section of the release notes describing differences between
SwissProt/EMBL format, this is listed:
* EMBL entry ID lines have an additional three-letter taxonomic division
'token' inserted between the data class and the molecule type;
I suppose we could use division() to store 'STANDARD' and 'PRELIMINARY' (or
'Swiss-Prot' and 'TrEMBL' if that's nicer).
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Daniel Lang
> Sent: Wednesday, September 06, 2006 4:12 AM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] retrieval of PRELIMINARY uniprot sequences using
> Bio::Registry fails
> Hi Brian,
> I'm iterating now over all uniprot_trembl sequences and record for which
> retrieval fails - Lets see if STANDARDs also fail...
> How is the second field of the swissprot ID line handled anyway? Because
> PRELIMINARYs end up as STANDARD when being parsed by Bio::SeqIO::swiss.
> On the other side I'm still confused why there's no error or warning
> when the retrieval fails. Can you give me a hint which modules (besides
> swiss.pm) to look at?
> Brian Osborne wrote:
> > Daniel,
> > Well, if you can isolate the bug please add it to bugzilla.
> > Brian O.
> > On 9/5/06 5:57 AM, "Daniel Lang" <daniel.lang at biologie.uni-freiburg.de>
> > wrote:
> >> Hi Brian,
> >> sorry for the belated response!
> >> I've compiled you a set of 100 PRELIMINARY entries from the latest
> >> uniprot_trembl release. I've tried to reproduce the bug using only
> >> as input to build an index, but (sadly) all of them can be retrieved
> >> using the latest checkout:-(
> >> Maybe its not connected to these entries after all, but the size or
> >> other feature of the uniprot distribution?
> >> I now could make it work using the 1.5.1 release.
> >> Originally, I've built the index using flat protocol, when I try bdb
> >> bioperl-live even more problems occur:
> >> bp_bioflat_index.pl --dbname sw -i bdb -f swiss -l . -c
> >> ------------- EXCEPTION -------------
> >> MSG: The lineage 'Eukaryota, Metazoa, Chordata, Craniata, Vertebrata,
> >> Euteleostomi, Amphibia, Batrachia, Anura, Mesobatrachia, Pipoidea,
> >> Pipidae, Xenopodinae, Xenopus, Silurana, Xenopus, tropicalis' had two
> >> non-consecutive nodes with the same name. Can't cope!
> >> STACK Bio::DB::Taxonomy::list::add_lineage
> >> /home/lang/bioperl/bioperl-live/Bio/DB/Taxonomy/list.pm:163
> >> STACK Bio::DB::Taxonomy::list::new
> >> /home/lang/bioperl/bioperl-live/Bio/DB/Taxonomy/list.pm:100
> >> STACK Bio::DB::Taxonomy::new
> >> /home/lang/bioperl/bioperl-live/Bio/DB/Taxonomy.pm:106
> >> STACK Bio::Species::classification
> >> /home/lang/bioperl/bioperl-live/Bio/Species.pm:171
> >> STACK Bio::SeqIO::swiss::_read_swissprot_Species
> >> /home/lang/bioperl/bioperl-live/Bio/SeqIO/swiss.pm:1049
> >> STACK Bio::SeqIO::swiss::next_seq
> >> /home/lang/bioperl/bioperl-live/Bio/SeqIO/swiss.pm:240
> >> STACK Bio::DB::Flat::parse_one_record
> >> /home/lang/bioperl/bioperl-live/Bio/DB/Flat.pm:333
> >> STACK Bio::DB::Flat::BDB::_index_file
> >> /home/lang/bioperl/bioperl-live/Bio/DB/Flat/BDB.pm:235
> >> STACK Bio::DB::Flat::BDB::build_index
> >> /home/lang/bioperl/bioperl-live/Bio/DB/Flat/BDB.pm:218
> >> STACK toplevel
> >> /share/apps/bioperl/bioperl-live/scripts_temp/bp_bioflat_index.pl:113
> >> But I think this is connected to the new changes to taxonomy handling
> >> Bio::Taxon...
> >> I'm unsure wether to submit this separately, but I could also provide
> >> example of such a swissprot entry that causes this error.
> >> Thanks, again.
> >> Daniel
> >> Brian Osborne wrote:
> >>> Daniel,
> >>> Bug, presumably in SeqIO/swiss.pm. Can you send me a small file with
> such a
> >>> PRELIMINARY entry?
> >>> Brian O.
> >>> On 9/1/06 6:11 AM, "Daniel Lang" <daniel.lang at biologie.uni-
> >>> wrote:
> >>>> 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
> >>>> 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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