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GENEPARSE

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 AT dna DOT bio DOT keio DOT ac DOT jp>

SEE ALSO

murasaki(1), geneparse(1)

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