SEQSPLIT(1) General Commands Manual SEQSPLIT(1)NAME
seqsplit - split seqs into chunks of defined size and overlap
SYNOPSIS
seqsplit [-options] <seqfile>
DESCRIPTION
This manual page documents briefly the seqsplit command.
seqsplit is a program that splits sequences into smaller chunks of defined size and overlap; output a FASTA file.
OPTIONS -h Help; display usage and version.
-o <file>
Output the new FASTA file to <file>.
--fragfile <f>
Save one-line-per-frag coord summary file to <f>.
--informat <s>
Specify sequence file format <s>.
--length <n>
Set max length of each unique seq frag to <n>.
--overlap <n>
Set overlap length to <n> (total frag size = length+overlap).
--shortnames
Use short "frag1" names, not "<src>/<from>-<to>".
LIMITATIONS
Still working in 32 bits -- no sequence can be more than 2 GB in size.
SEE ALSO afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1),
weight(1).
AUTHOR
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
This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,
for the Debian project (but may be used by others).
Mon, 01 Aug 2005 15:28:08 -0300SEQSPLIT(1)
Check Out this Related Man Page
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 align-
ment 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
Biosquid 1.9g January 2003 seqstat(1)