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
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
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.
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),
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.
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
FAX : 1-314-362-2157