This file is indexed.

/usr/bin/bp_pairwise_kaks is in bioperl 1.6.924-1.

This file is owned by root:root, with mode 0o755.

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
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
#!/usr/bin/perl 

eval 'exec /usr/bin/perl  -S $0 ${1+"$@"}'
    if 0; # not running under some shell
use strict;
use warnings;
# Author Jason Stajich <jason-at-bioperl-dot-org>

=head1 NAME

bp_pairwise_kaks - script to calculate pairwise Ka,Ks for a set of sequences

=head1 SYNOPSIS

bp_pairwise_kaks.PLS -i t/data/worm_fam_2785.cdna [-f fasta/genbank/embl...] [-msa tcoffee/clustal] [-kaks yn00/codeml]

=head1 DESCRIPTION 

  This script will take as input a dataset of cDNA sequences verify
 that they contain no stop codons, align them in protein space,
 project the alignment back into cDNA and estimate the Ka
 (non-synonymous) and Ks (synonymous) substitutions based on the ML
 method of Yang with the PAML package.

 Requires:
 * bioperl-run package
 * PAML program codeml or yn00
 * Multiple sequence alignment programs Clustalw OR T-Coffee

 Often there are specific specific parameters you want to run when you
 a computing Ka/Ks ratios so consider this script a starting point and
 do not rely it on for every situation.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

 Jason Stajich jason-at-bioperl-dot-org

=cut

eval {
    # Ka/Ks estimators
    require Bio::Tools::Run::Phylo::PAML::Codeml;
    require Bio::Tools::Run::Phylo::PAML::Yn00;
    
    # Multiple Sequence Alignment programs
    require Bio::Tools::Run::Alignment::Clustalw;
    require Bio::Tools::Run::Alignment::TCoffee;
};
if( $@ ) {
    die("Must have bioperl-run pkg installed to run this script");
}
# for projecting alignments from protein to R/DNA space
use Bio::Align::Utilities qw(aa_to_dna_aln);

# for input of the sequence data
use Bio::SeqIO;
use Bio::AlignIO;

# for the command line argument parsing
use Getopt::Long;

my ($aln_prog, $kaks_prog,$format, $output,
    $cdna,$verbose,$help) = qw(clustalw codeml fasta);

GetOptions(
	   'i|input:s'      => \$cdna,
	   'o|output:s'     => \$output,
	   'f|format:s'     => \$format,
	   'msa:s'          => \$aln_prog,
	   'kaks:s'         => \$kaks_prog,
	   'v|verbose'      => \$verbose,
	   'h|help'         => \$help,
	   );

if( $help ) {
    exec('perldoc',$0);
    exit(0);
}
$verbose = -1 unless $verbose;
my ($aln_factory,$kaks_factory);
if( $aln_prog =~ /clus/i ) {
    $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new(-verbose => $verbose);
} elsif( $aln_prog =~ /t\_?cof/i ) {
    $aln_factory = Bio::Tools::Run::Alignment::TCoffee->new(-verbose => $verbose);
} else { 
    warn("Did not provide either 'clustalw' or 'tcoffee' as alignment program names");
    exit(0);
}
unless( $aln_factory->executable ) {
    warn("Could not find the executable for $aln_prog, make sure you have installed it and have either set ".uc($aln_prog)."DIR or it is in your PATH");
    exit(0);
}


if( $kaks_prog =~ /yn00/i ) {
    $kaks_factory = Bio::Tools::Run::Phylo::PAML::Yn00->new(-verbose => $verbose);
} elsif( $kaks_prog =~ /codeml/i ) {
    # change the parameters here if you want to tweak your Codeml running!
    $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new
	(-verbose => $verbose,
	 -params => { 'runmode' => -2,
		      'seqtype' => 1,
		  }
	 );
}
unless ( $kaks_factory->executable ) {
    warn("Could not find the executable for $kaks_prog, make sure you have installed it and you have defined PAMLDIR or it is in your PATH");
    exit(0);
}

unless ( $cdna && -f $cdna && -r $cdna &&  ! -z $cdna ) {
    warn("Did not specify a valid cDNA sequence file as input"); 
    exit(0);
}

my $seqin = new Bio::SeqIO(-file   => $cdna, 
			   -format => $format);

my %seqs;
my @prots;
while( my $seq = $seqin->next_seq ) {
    $seqs{$seq->display_id} = $seq;
    my $protein = $seq->translate();
    my $pseq = $protein->seq();
    
    $pseq =~ s/\*$//;
    if( $pseq =~ /\*/ ) {
	warn("provided a cDNA (".$seq->display_id.") sequence with a stop codon, PAML will choke!");
	exit(0);
    }
    # Tcoffee can't handle '*'
    $pseq =~ s/\*//g;
    $protein->seq($pseq);
    push @prots, $protein;
}
if( @prots < 2 ) {
    warn("Need at least 2 cDNA sequences to proceed");
    exit(0);
}

local * OUT;
if( $output ) {
    open(OUT, ">$output") || die("cannot open output $output for writing");
} else { 
    *OUT = *STDOUT;
}

my $aa_aln = $aln_factory->align(\@prots);
my $dna_aln = &aa_to_dna_aln($aa_aln, \%seqs);

my @each = $dna_aln->each_seq();


$kaks_factory->alignment($dna_aln);

my ($rc,$parser) = $kaks_factory->run();
if( $rc <= 0 ) { 
    warn($kaks_factory->error_string,"\n");
    exit;
}
my $result = $parser->next_result;

if ($result->version =~ m/3\.15/) {
	warn("This script does not work with v3.15 of PAML!  Please use 3.14 instead.");
	exit(0);
}

my $MLmatrix = $result->get_MLmatrix();

my @otus = $result->get_seqs();

my @pos = map { 
    my $c= 1;
    foreach my $s ( @each ) {
	last if( $s->display_id eq $_->display_id );
	$c++;
    }
    $c; 
} @otus; 

print OUT join("\t", qw(SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID)), "\n";
for( my $i = 0; $i < (scalar @otus -1) ; $i++) {
    for( my $j = $i+1; $j < (scalar @otus); $j++ ) {
	my $sub_aa_aln = $aa_aln->select_noncont($pos[$i],$pos[$j]);
	my $sub_dna_aln = $dna_aln->select_noncont($pos[$i],$pos[$j]);
	print OUT join("\t",  
		       $otus[$i]->display_id,
		       $otus[$j]->display_id,$MLmatrix->[$i]->[$j]->{'dN'},
		       $MLmatrix->[$i]->[$j]->{'dS'},
		       $MLmatrix->[$i]->[$j]->{'omega'},
		       sprintf("%.2f",$sub_aa_aln->percentage_identity),
		       sprintf("%.2f",$sub_dna_aln->percentage_identity),
		       ), "\n";
    }
}