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

-h

display the list of commands.
-v

get version
-conf

specify configuration file
-s

sequence file to analyse.
-g

grammar file to analyse
-m

model file to analyse
-check

check a grammar, no execution. Requires -g
-dna

analyse dna, is default
-rna

analyse rna
-protein

analyse protein
-max

maximum returned solutions
-all

analyse both directions of the sequence
-output

output file name, must be unique

OTHER OPTIONS

-sequenceID

position of sequence in bank
-uid

Use a defined identifier for the query
-lmax

maximum length of a variable
-maxspacer

maximum size of a spacer
-offset

Offset value to add to positions
-start

Start position on sequence
-end

End position on sequence
-noclean

Do not delete created files after treatment (for debug)
-enabledups

enable duplicate result matches. By default only keep singletons
-filter

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

minimum length of a variable (to speedup parsing)
-c

maximum size of a match (to speedup parsing)
-maxres

maximum result size of a match (to speedup parsing)

AUTHOR

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