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LogolExec(1) USER COMMANDS LogolExec(1)

NAME

LogolExec - Program to parse a logol grammar and search pattern in a sequence.

SYNOPSIS

LogolExec [-h]

INSTALLATION


Logol requires the Cassiopee Ruby gem. To install it run:
gem install cassiopee

CONFIGURATION


LogolExec use a default configuration file in /etc/logol/logol.properties. It is possible to specify a different configuration file via command-line. Temporary and results directory must be writable by the user.
By default, /var/lib/logol/results contains generated results and /tmp is used at temporary directory.
.PP

OPTIONS


Minimum arguments are -m for logol model or -g for logol grammar, and -s for input sequence

MAIN OPTIONS


display the list of commands.

get version

specify configuration file

sequence file to analyse.

grammar file to analyse

model file to analyse

check a grammar, no execution. Requires -g

analyse dna, is default

analyse rna

analyse protein

maximum returned solutions

analyse both directions of the sequence

output file name, must be unique

OTHER OPTIONS


position of sequence in bank

Use a defined identifier for the query

maximum length of a variable

maximum size of a spacer

Offset value to add to positions

Start position on sequence

End position on sequence

Do not delete created files after treatment (for debug)

enable duplicate result matches. By default only keep singletons

Type of filter when enabledups is not enabled. Allowed types are exact(default),local,local0,global.

minimum length of a variable (to speedup parsing)

maximum size of a match (to speedup parsing)

maximum result size of a match (to speedup parsing)

AUTHOR

Olivier Sallou (olivier.sallou (at) irisa.fr)

September 28, 2011 version 1.0