/usr/bin/bp_pairwise_kaks is in bioperl 1.6.924-3.
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";
}
}
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