bionic (1) seqstat.1.gz

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