LogolExec1
Program to parse a logol grammar and search pattern in a sequence.
Usage
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
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-check -
check a grammar, no execution. Requires -g
-
-dna -
analyse dna, is default
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-rna -
analyse rna
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-protein -
analyse protein
-
-max -
maximum returned solutions
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-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
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-start -
Start position on sequence
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-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)
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-c -
maximum size of a match (to speedup parsing)
-
-maxres -
maximum result size of a match (to speedup parsing)
Releases
Unchanged in 5 releases since Debian 8 (Jessie).