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 [email protected]: > 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 [email protected] http://www.plantco.de/people/Oliver.html MOSS 2011 - the annual meeting on bryophyte research http://plantco.de/MOSS2011/ _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
