LogolExec [-h]


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


LogolExec use a default configuration file in /etc/logol/ 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


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



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



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)


Olivier Sallou (olivier.sallou (at)