[EMBOSS] seqret does not find sequence after update

[Oliver Liegmann]

Hello,

thank you very much for your reply. dbifasta with "C" locales and
dbxfasta both seem to work well.

To answer your question: The operating system is Ubuntu 10.04 (Lucid)
with locales set to de_DE.utf8.

Best regards,
Oliver Liegmann

P.S.: I CC'ed this message to the list, for other users to know about
the workaround. Probably a short note should be written into the
documentation of dbifasta about the locales issue.

Am Freitag, den 04.02.2011, 19:34 +0000 schrieb ajb at ebi.ac.uk: 
> Hello,
> 
> I could reproduce your problem. It appears to be a manifestation of the
> GNU sort "sorting order". If you, depending on your shell, do:
> 
>   export LC_ALL=C
> 
> or
> 
>   setenv LC_ALL C
> 
> and then re-index using dbifasta then retrieval should work as expected.
> Alternatively use to dbx indexing system which does not rely on
> GNU sort.
> 
> Incidentally, what operating system and version are you using?
> 
> HTH
> 
> Alan Bleasby
> EBI
> 
> 
> 
> > Dear list members,
> >
> > does some of you also got this problem (and probably has an idea on what's
> > going wrong):
> >
> > After upgrading from version 6.2.0 to 6.3.1 seqret does not work
> > properly anymore:
> > First, Emboss was installed using
> > ./configure --enable-64 --prefix=/opt/emboss
> > make
> > make install
> >
> > The database was set up with:
> > dbifasta -dbname plafa -idformat simple -filenames PLAFA_test.fas
> >
> > Using seqret to retrieve the sequences produces an error:
> > seqret plafa_test:PLAFA_MAL13P1.23-b
> > Reads and writes (returns) sequences
> > output sequence(s) [plafa_mal13p1.fasta]:
> > Error: Failed to read sequence 'plafa:PLAFA_MAL13P1.237a'
> >
> > Only the remaining two sequences are stored in the output file.
> >
> > Are the allowed characters used in the accession changed? With Emboss
> > 6.2.0 we did not have any problems, but after upgrade a huge bunch of
> > sequences could not be retrieved anymore when used with our internal fasta
> > database, although the output in
> > outfile.dbifasta shows all sequences to be inserted into the database.
> >
> >
> > The content of the different files are:
> > PLAFA_test.fas:
> >>PLAFA_MAL13P1.23-b
> > MLTCFLFYIYEKKASNKKYDYDEIDLNDDDDDIIDNKSFDKNNYSYNIKNRLFKHYKKVH
> >>PLAFA_MAL13P1.237a
> > MKNTFFFVLSFFLYITILDITLTSLIQKNILKEKVDKEYMKVFLFVNNSQKYCEKDNIIL
> >>PLAFA_MAL13P1.23-a
> > MSFESFVLKDEKKASNKKYDYDEIDLNDDDDDIIDNKSFDKNNYSYNIKNRLFKHYKKVH
> >
> >
> > test.txt:
> > plafa:PLAFA_MAL13P1.23-b
> > plafa:PLAFA_MAL13P1.237a
> > plafa:PLAFA_MAL13P1.23-a
> >
> >
> > emboss.default:
> > DB plafa [
> > 	format: fasta
> > 	method: emblcd
> > 	directory: /home/liegmann/genomezoo/emboss/prob/test/db
> > 	type: P
> > ]
> >
> >
> >
> > Best regards,
> > Oliver Liegmann


-- 
Dipl.-Inf. Oliver Liegmann

AG Rensing
Fakultät für Biologie
Albert-Ludwigs-Universität Freiburg
Hauptstraße 1
D-79104 Freiburg

+49 761 203-2521
oliver.liegmann at biologie.uni-freiburg.de
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