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)
AUTHOR¶
Kris Popendorf <krisp@dna.bio.keio.ac.jp>