table of contents
| LogolExec(1) | USER COMMANDS | LogolExec(1) |
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)
| September 28, 2011 | version 1.0 |