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
outfile.dbifasta
Description: Binary data
_______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
