sindex(1)							  Biosquid Manual							 sindex(1)

NAME

       sindex - index a sequence database for sfetch

SYNOPSIS

       sindex [options] seqfile1 [seqfile2...]

DESCRIPTION

       sindex  indexes one or more seqfiles for future sequence retrievals by sfetch.  An SSI ("squid sequence index") file is created in the same
       directory with the sequence files. By default, this file is called <seqfile>.ssi.

       If there is more than one sequence file on the command line, the SSI filename will be constructed from the last sequence  file  name.  This
       may not be what you want; see the -o option to specify your own name for the SSI file.

       sindex  is  capable of indexing large files (>2 GB) if optional LFS support has been enabled at compile-time. See INSTALL instructions that
       came with @PACKAGE@.

OPTIONS

       -h     Print brief help; includes version number and summary of all options, including expert options.

       -o <ssi outfile>
	      Direct the SSI index to a file named <outfile>.  By default, the SSI file would go to <seqfile>.ssi.

EXPERT OPTIONS

       --64   Force the SSI file into 64-bit (large seqfile) mode, even if the seqfile is small. You don't want to do this  unless  you're  debug-
	      ging.

       --external
	      Force sindex to do its record sorting by external (on-disk) sorting. This is only useful for debugging, too.

       --informat <s>
	      Specify  that  the sequence file is definitely in format <s>; blocks sequence file format autodetection. This is useful in automated
	      pipelines, because it improves robustness (autodetection can occasionally go wrong on a perversely misformed file). Common  examples
	      include  genbank,  embl, gcg, pir, stockholm, clustal, msf, or phylip; see the printed documentation for a complete list of accepted
	      format names.

       --pfamseq
	      A hack for Pfam; indexes a FASTA file that is known to have identifier lines in format ">[name] [accession] [optional description]".
	      Normally	only the sequence name would be indexed as a primary key in a FASTA SSI file, but this allows indexing both the name (as a
	      primary key) and accession (as a secondary key).

SEE ALSO

       afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1),	seqsplit(1),  seqstat(1),  sfetch(1),  shuffle(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 							 sindex(1)