SIMPLE SOLUTIONS

SEQSTAT(1) - man page online | user commands

Show statistics and format for a sequence file.

Chapter
January 2003
seqstat(1)                               Biosquid Manual                               seqstat(1)

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 for‐ mat. 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 COPY‐ ING 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: @genetics.wustl.edu
Biosquid 1.9g January 2003 seqstat(1)
This manual Reference Other manuals
seqstat(1) referred by afetch(1) | alistat(1) | compalign(1) | compstruct(1) | revcomp(1) | seqsplit(1) | sfetch(1) | shuffle(1) | sindex(1) | sreformat(1) | stranslate(1) | weight(1)
refer to afetch(1) | alistat(1) | compalign(1) | compstruct(1) | revcomp(1) | seqsplit(1) | sfetch(1) | shuffle(1) | sindex(1) | sreformat(1) | stranslate(1) | weight(1)