- 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
- 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.
- Print brief help; includes version number and summary of all options,
including expert options.
- (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.
- 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
HHMI/Department of Genetics
Washington University School of Medicine
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St Louis, MO 63108 USA
FAX : 1-314-362-2157