Thank you very much for your advises. http://emboss.sourceforge.net/docs/themes/Databases.html I made the two configuration files (emboss.default & .embossrc) and "showdb" showed the database, but the commands (entret, seqret, & whichdb) don't work. The details are described below.
------------------------------------------- http://emboss.sourceforge.net/docs/themes/Databases.html#default The emboss.default file (1) emboss.default (share/EMBOSS) $ cd /usr/local/share/EMBOSS $ su # cp emboss.default.template emboss.default (2) .embossrc (personal home directory) .embossrc set emboss_acdroot /usr/local/share/EMBOSS/acd http://emboss.sourceforge.net/docs/themes/Databases.html#test Testing the database definitions (run showdb) $showdb Displays information on the currently available databases # Name Type ID Qry All Comment # ==== ==== == === === ======= tpir P OK OK OK PIR using NBRF access for 4 files tsw P OK OK OK Swissprot native format with EMBL CD- ROM index tswnew P OK OK OK Swissnew as 3 files in native format with EMBL CD-ROM index twp P OK OK OK EMBL new in native format with EMBL CD- ROM index tembl N OK OK OK EMBL in native format with EMBL CD-ROM index tgb N OK - - Genbank IDs tgenbank N OK OK OK GenBank in native format with EMBL CD- ROM index http://www.csc.fi/molbio/progs/emboss/doc/programs/html/entret.html $entret tembl:hsfau Reads and writes (returns) flatfile entries Warning: Cannot open division file '<null>' for database 'tembl' Warning: seqCdQry failed Error: Unable to read sequence 'tembl:hsfau' Died: entret terminated: Bad value for '-sequence' and no prompt http://www.csc.fi/molbio/progs/emboss/doc/programs/html/seqret.html $seqret Reads and writes (returns) sequences Input sequence(s): tembl:hsfau Warning: Cannot open division file '<null>' for database 'tembl' Warning: seqCdQry failed Error: Unable to read sequence 'tembl:hsfau' Input sequence(s): http://www.csc.fi/molbio/progs/emboss/doc/programs/html/whichdb.html $whichdb -showall Search all databases for an entry ID or Accession number: hsfau1 Output file [outfile.whichdb]: stdout # Trying 'twp:hsfau1' Warning: Cannot open division file '<null>' for database 'twp' Warning: seqCdQry failed # Failed 'twp:hsfau1' # Trying 'tsw:hsfau1' Warning: Cannot open division file '<null>' for database 'tsw' Warning: seqCdQry failed # Failed 'tsw:hsfau1' # Trying 'tgenbank:hsfau1' Warning: Cannot open division file '<null>' for database 'tgenbank' Warning: seqCdQry failed # Failed 'tgenbank:hsfau1' # Trying 'tpir:hsfau1' Warning: Cannot open division file '<null>' for database 'tpir' EMBOSS An error in ajseqdb.c at line 5141: seqCdQryOpen failed ------------------------------------------- Haruo Suzuki http://emboss.open-bio.org/pipermail/emboss/2006-July/002561.html -------------------------------------- Let's start Yahoo! Auction - Free Campaign Now! http://pr.mail.yahoo.co.jp/auction/ _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
