[EMBOSS] difficulty using databases and "water"
Scott Markel
smarkel at scitegic.com
Fri Sep 10 17:23:24 UTC 2004
I'm using 2.9.0, built in cygwin, running in Windows XP.
I'm having problems creating databases for use with "water".
I created a USA database using dbifasta.
133 > dbifasta -idformat idacc -directory /C/SandBox/EMBOSS -filenames NRDB_protein_10.* -dbname NRDB_protein_10 -release 1.0 -date "10/09/04" -fields acnum -fields des -fields seqvn
Index a fasta database
I edited ~/.embossrc to include the new database.
134 > cat ~/.embossrc
DB NRDB_protein_10 [
type: P
format: fasta
method: emblcd
fields: "id acc sv des"
directory: /C/SandBox/EMBOSS
indexdirectory: /C/SandBox/EMBOSS
file: NRDB_protein_10.fa
]
showdb does the right thing.
135 > showdb
Displays information on the currently available databases
# Name Type ID Qry All Comment
# ==== ==== == === === =======
NRDB_protein_10 P OK OK OK -
seqret can access all of the database.
136 > seqret NRDB_protein_10:\* stdout
Reads and writes (returns) sequences
>XP_357594.1 XP_357594.1 similar to KIAA0960 protein [Mus musculus]
MCFPGEEVDRQLCRDAIFPIPVACDAPCPKDCVLSAWSSWSSCSHTCSGKTTEGKQTRAR
<shows all 10 sequences just fine>
I can't seem to access an individual sequence.
137 > seqret NRDB_protein_10:XP_357594
Reads and writes (returns) sequences
Error: Unable to read sequence 'NRDB_protein_10:XP_357594'
Died: seqret terminated: Bad value for '-sequence' and no prompt
What I'm really trying to do is run "water", but I expect
my database problems are impacting that.
161 > water -asequence query.fa -bsequence NRDB_protein_10:\*
Smith-Waterman local alignment.
EMBOSS An error in ajarr.c at line 1805:
Token missing
Any pointers to documentation or examples would be greatly
appreciated.
Scott
--
Scott Markel, Ph.D.
Principal Bioinformatics Architect email: smarkel at scitegic.com
SciTegic Inc. mobile: +1 858 205 3653
9665 Chesapeake Drive, Suite 401 voice: +1 858 279 8800, ext. 253
San Diego, CA 92123 fax: +1 858 279 8804
USA web: http://www.scitegic.com
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