Program to parse a logol grammar and search pattern in a sequence.
Logol requires the Cassiopee Ruby gem. To install it run: gem install cassiopee
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
Minimum arguments are -m for logol model or -g for logol grammar, and -s for input sequence
display the list of commands.
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
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) irisa.fr)