geneparse(1) 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.


use soft-repeatmasked sequences (ie: replace lowercase bases with N's).
 uppercase all bases.
just print the length and exit
don't append a new line when finished
prints the program version
prints a help message
send output to a file (otherwise use stdout). --output implies --clean.
silence all warnings
prints lots of extra details


GNU General Public License, version 3 (GPLv3)


Kris Popendorf <[email protected]>