geneparse1

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

Overview

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