afetch(1)							  Biosquid Manual							 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), strans-
       late(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

Biosquid 1.9g							   January 2003 							 afetch(1)