geneparse − sequence file loader frontend
geneparse [options...] [input] [input2 ...] #read input and write to stdout
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.
−−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
GNU General Public License, version 3 (GPLv3)
<http://murasaki.sourceforge.net>
Kris Popendorf <krisp AT dna DOT bio DOT keio DOT ac DOT jp>