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geneparse - sequence file loader frontend

GENEPARSE(1) User Contributed Perl Documentation GENEPARSE(1)

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 <krisp@dna.bio.keio.ac.jp>

SEE ALSO

murasaki(1), geneparse(1)
2010-05-31 perl v5.10.1