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)