/usr/share/perl5/PAI_scripts/help.pm is in alien-hunter 1.7-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | =head1 NAME
PAI_scripts::help
=head1 SYNOPSIS
provides help info to the user
=head1 AUTHOR
George Vernikos <gsv(at)sanger.ac.uk>
=head1 LICENSE
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
=cut
package PAI_scripts::help;
use Exporter;
@ISA = ("Exporter");
@EXPORT = qw (&help);
sub help{
print "\n----------------------------\n\talien_hunter [Release 1.7] \n\n\tINPUT: raw genomic sequence PREDICTION: HGT regions based on Interpolated Variable Order Motifs (IVOMs)
arguments:
[<sequence.file>]
[<output.file>]
(optional):
[-a] to load the prediction file into Artemis
[-c] optimize predicted boundaries with a change-point detection 2 state 2nd order HMM
output:
<output.file> predictions (tab file) in embl format
<output.file.opt> optimized (HMM) predictions (tab file) in embl format
<output.file.plot> predictions in Artemis User Plot format to be loaded manually using Graph -> Add User Plot...
<output.file.opt.plot> optimized (HMM) predictions in Artemis User Plot format to be loaded manually using Graph -> Add User Plot...
<output.file.sco> the scores over all the sliding windows - for score distribution check
Note: Predictions that overlap with rRNA operon are mentioned in the note qualifier
------------------------\n";
}
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