NAME
seqstat - show statistics and format for a sequence file
SYNOPSIS
seqstat [options] seqfile
DESCRIPTION
seqstat reads a sequence file seqfile and shows a number of simple
statistics about it.
The printed statistics include the name of the format, the residue type
of the first sequence (protein, RNA, or DNA), the number of sequences,
the total number of residues, and the average and range of the sequence
lengths.
OPTIONS
-a Show additional verbose information: a table with one line per
sequence showing name, length, and description line. These
lines are prefixed with a * character to enable easily grep’ing
them out and sorting them.
-h Print brief help; includes version number and summary of all
options, including expert options.
-B (Babelfish). Autodetect and read a sequence file format other
than the default (FASTA). Almost any common sequence file format
is recognized (including Genbank, EMBL, SWISS-PROT, PIR, and GCG
unaligned sequence formats, and Stockholm, GCG MSF, and Clustal
alignment formats). See the printed documentation for a complete
list of supported formats.
EXPERT OPTIONS
--informat <s>
Specify that the sequence file is in format <s>, rather than the
default FASTA format. Common examples include Genbank, EMBL,
GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed
documentation for a complete list of accepted format names.
This option overrides the default expected format (FASTA) and
the -B Babelfish autodetection option.
--quiet
Suppress the verbose header (program name, release number and
date, the parameters and options in effect).
SEE ALSO
afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1),
seqsplit(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