SYNAPSE

geneparse [options...] [input] [input2 ...] #read input and write to stdout

DESCRIPTION

Reads a sequence file and writes it somewhere (by default to stdout).

A specific range within an input file can be specified by file[start,stop]. The square brackets can be interchanged for any of {[()]}, (eg. ``genome.fa[3000,4000]'' or ``genome.fa{3000~4000}''). Be aware that all of those might be parsed by your shell. Also any non-word character can be used to separate the numbers.

OPTIONS

--repeatmask|-r

use soft-repeatmasked sequences (ie: replace lowercase bases with N's).

--upper|--unmask|-U

 uppercase all bases.

--length|-l

just print the length and exit

--clean|-c

don't append a new line when finished

--version|-V

prints the program version

--help|-h

prints a help message

--output|-o

send output to a file (otherwise use stdout). --output implies --clean.

--quiet|-q

silence all warnings

--verbose|-v

prints lots of extra details

LICENSE

GNU General Public License, version 3 (GPLv3)

AVAILABILITY

<http://murasaki.sourceforge.net>

AUTHOR

Kris Popendorf <[email protected]>