- afetch - retrieve an alignment from an alignment
database
-
afetch [options] alignmentdb key
afetch --index alignmentdb
afetch retrieves the alignment named
key from an alignment
database in file
alignmentdb.
alignmentdb is a "multiple multiple alignment" file in
Stockholm (e.g. native Pfam) format.
key is either the name (ID) of the alignment, or its accession number
(AC).
The
alignmentdb file should first be SSI indexed with
afetch
--index for efficient retrieval. An SSI index is not required, but
alignment retrieval without one may be painfully slow.
- -h
- Print brief help; includes version number and summary of
all options, including expert options.
- --index
- Instead of retrieving a key, the special command
afetch --index alignmentdb produces an SSI index of the
names and accessions of the alignments in the file alignmentdb.
This should be run once on the alignmentdb file to prepare it for
all future afetch's.
alistat(1),
compalign(1),
compstruct(1),
revcomp(1),
seqsplit(1),
seqstat(1),
sfetch(1),
shuffle(1),
sindex(1),
sreformat(1),
stranslate(1),
weight(1).
Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington
University School of Medicine Freely distributed under the GNU General Public
License (GPL) See COPYING in the source code distribution for more details, or
contact me.
Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX : 1-314-362-2157
Email: [email protected]