LogolExec

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)