NAME
geneparse - sequence file loader frontend
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]>