- seqstat - show statistics and format for a sequence
file
-
seqstat [options] seqfile
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.
- -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.
-
--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).
afetch(1),
alistat(1),
compalign(1),
compstruct(1),
revcomp(1),
seqsplit(1),
sfetch(1),
shuffle(1),
sindex(1),
sreformat(1),
stranslate(1),
weight(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.
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: [email protected]