/usr/share/perl5/PAI_scripts/rrna.pm is in alien-hunter 1.7-2.
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 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 | =head1 NAME
PAI_scripts::rrna
=head1 SYNOPSIS
Annotates alien_hunter predictions that overlap with a 16s 102bp rRNA motif;
This motif comes from a consensus of 16s rRNA alignment from:
Ecoli 223771:225312 forward
Mycobacterium 1341144:1342692 forward
Neisseria 198339:199883 reverse
Pseudomonas 722096:723631 forward
Rhizobium 2750005:2751465 reverse
Ricketsia 772263:773769 reverse
Salmonella 287479:289020 forward
Staph 514251:515805 forward
Streptococcus 17043:18549 forward
Thermotoga 188968:190526 forward
Vibrio 53823:55357 forward
Bacillus 9809:11361 forward
Chlamydia 856874:858423 forward
Clostridium 8715:10223 reverse
Corynebacterium 76643:78166 forward
Campylobacter 39249:40761 forward
Mycoplasma 170007:171525 forward
=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::rrna;
use Exporter;
@ISA = ("Exporter");
@EXPORT = qw (&rrna &overlapRNA);
sub rrna{
$GenSeq=$_[0];
$GenSeq=uc($GenSeq);
#forward strand:
$_=$GenSeq;
while(/(ACA..GG.ACTGAGA.AC.G.CC..ACTC.{0,1}TACGGGAGGC.GCAGT.G.GAAT.TT...CAATG...G.AA...TGA...AGC.A..CCG.GTG...GA.GA)/g){
$to=pos($_);
$len=length($1);
$from=$to-$len+1;
$loc{$from}=$to;
print " possible rRNA signature: $from..$to\n";
}
#reverse strand:
$_=$GenSeq;
while(/(TC.TC...CAC.CGG..T.GCT...TCA...TT.C...CATTG...AA.ATTC.C.ACTGC.GCCTCCCGTA.{0,1}GAGT..GG.C.GT.TCTCAGT.CC..TGT)/g){
$to=pos($_);
$len=length($1);
$from=$to-$len+1;
$loc{$from}=$to;
print " possible rRNA signature: $from..$to\n";
}
return();
}
1;
sub overlapRNA{
$from=$_[0];
$to=$_[1];
$check=0;
foreach $k (keys %loc){
if(($k>=$from) & ($k<$to)){
$check=1;
}
elsif(($loc{k}>$from) & ($loc{k}<=$to)){
$check=1;
}
}
return($check);
}
1;
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