afetch(1)
NAME
afetch - retrieve an alignment from an alignment database
SYNOPSIS
afetch [options] alignmentdb key afetch --index alignmentdb
DESCRIPTION
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.
OPTIONS
- -h Print brief help; includes version number and summary of all
- options, including expert options.
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.
SEE ALSO
alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1),
weight(1).
AUTHOR
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: eddy@genetics.wustl.edu