Program to parse a logol grammar and search pattern in a sequence.
LogolExec [-h]
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
-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
-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)
Olivier Sallou (olivier.sallou (at) irisa.fr)