/usr/share/augustus/scripts/prints2prfl.pl is in augustus 3.3+dfsg-2build1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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################################################################################
#
# Name: prints2prfl.pl
# Project: Gene Prediction with Protein Family Patterns
# Author: Oliver Keller
# Date: 2011-01-03
# Version: 0.1
#
#
# prints2prfl.pl [<options>] <MSA>
#
# Converts a PRINTS database flat file into a set of block profiles
# that can be used as input for AUGUSTUS-PPX.
#
# Uses a BLOSUM matrix to calculate pseudocounts. Ensure that
# the variable AUGUSTUS_CONFIG_PATH is set in order to make that work.
#
use strict;
use Getopt::Long;
use List::Util "sum";
my %data;
my $MIN_WIDTH = 6;
my $REG_MATR_FILE;
my $WEIGHTING_MODE="none";
my $DEFAULT_GLOB_WEIGHT=20;
my $GLOB_WEIGHT;
my $AMINO_ACIDS = "GDERKNQSTAVLIFYWHMCP";
my $QIJ_ORDER = "ARNDCQEGHILKMFPSTWYV";
my @AA_LIST = split "", $AMINO_ACIDS;
my $MAX_ENTROPY;
my $MIN_CONSERVE;
my $DISABLE_WEIGHTS;
my $AA_COUNT = length($AMINO_ACIDS);
my $LOG20 = log($AA_COUNT);
my $INITARGS = join(" ", @ARGV);
my $regmatrix;
### subroutines
#
# read in the qij (regularisation) matrix
#
sub read_qij {
my $fh = shift;
my @SM_AAS = ();
my $matrix = {};
my $sm_count=0;
while (<$fh>) {
chomp;
s/\#.*$//;
s/^\s*|\s*$//g;
next if (/^$/);
unless (@SM_AAS) {
my $FILE_AAS=uc;
$FILE_AAS =~ s/[^A-Z]//g;
my $patt = '^['.$FILE_AAS.']*$';
if (length($FILE_AAS)==20 && $AMINO_ACIDS =~ /$patt/) {
@SM_AAS = split "", $FILE_AAS;
next;
} else {
@SM_AAS = split "", $QIJ_ORDER;
}
}
my @line = split(/\s+/);
if (@line <= $sm_count || @line > 20 || grep { !/^\d+\.\d*$|^\.\d+$/ } @line) {
print STDERR "Not a valid frequency file!\n";
return;
}
@{$matrix->{$SM_AAS[$sm_count]}}{@SM_AAS} = @line;
$sm_count++;
last if ($sm_count == 20);
}
# normalizing - the substitution matrix (SM) is scaled the following way:
# - it is made symmetric by substituting SM_ij and SM_ji with (SM_ij+SM_ji/2)
# - every entry is divided by the total sum of all entries
my $sm_sum=0;
foreach (0..$#SM_AAS) {
my $aa1 = $SM_AAS[$_];
foreach my $aa2 (@SM_AAS[0..$_-1]) {
my $ref1 = \$matrix->{$aa1}{$aa2};
unless (defined $matrix->{$aa2}{$aa1}) {
$matrix->{$aa2}{$aa1} = $$ref1;
} else {
my $ref2 = \$matrix->{$aa2}{$aa1};
my $val = ($$ref1 + $$ref2)/2;
$$ref1 = $$ref2 = $val;
}
$sm_sum += 2 * $$ref1;
}
$sm_sum += $matrix->{$aa1}{$aa1};
}
foreach (@SM_AAS) {
foreach my $aa2 (@SM_AAS) {
$matrix->{$_}{$aa2} /= $sm_sum;
}
$matrix->{"*"}{$_} = sum(@{$matrix->{$_}}{@SM_AAS});
}
$regmatrix=$matrix;
}
sub calculate_pssm {
#### change this according to msa2prfl
my $blockref = shift;
my ($size, $height) =
@$blockref{"width", "height"};
my $result = { "lines" => [] };
unless ($DISABLE_WEIGHTS) {
$blockref->{weights} = [ (0) x $height ];
foreach (@{$blockref->{columns}}) {
my $frq = $_->{frq};
my @res = grep { /^[$AMINO_ACIDS]$/ } keys %$frq;
my %colweights = map { ( $_ => 0 ) } keys %$frq;
@colweights{@res} = map { 1/$frq->{$_}/(scalar @res) } @res;
my $i=0;
foreach my $c (@{$_->{str}}) {
$blockref->{weights}[$i++] += $colweights{$c};
}
}
$_ /= $blockref->{width} foreach (@{$blockref->{weights}});
}
my @entropies;
foreach (@{$blockref->{columns}}) {
my $freq = $_->{frq};
unless ($DISABLE_WEIGHTS) {
%$freq = ();
foreach my $i (0..$height-1) {
$freq->{$_->{str}[$i]} += $blockref->{weights}[$i];
}
} else {
$_ /= $height foreach values %$freq;
delete $freq->{$_} foreach grep { /[^$AMINO_ACIDS]/ } keys %$freq;
}
# substitute non-standard keys
# U -> [C] O->[K]
# B -> [DN] J->[IL]
# Z -> [EQ] X->(any)
foreach ( ["U","C"], ["B","D","N"], ["Z","E","Q"],
["O", "K"], ["J", "I", "L"], ["X", @AA_LIST] ) {
next unless exists $freq->{$_->[0]};
my $rem = $freq->{$_->[0]};
delete $freq->{shift @$_};
my @freqs = @{$regmatrix->{"*"}}{@$_};
my $factor = $rem / sum(@freqs);
foreach (@$_) {
$freq->{$_} += (shift @freqs)*$factor;
}
}
### DEBUG
if (keys %$freq > $AA_COUNT) {
die "Have keys '".join("", sort keys %$freq,)."'\nshould have '".join("", sort @AA_LIST)."'";
}
if (abs(sum (values %$freq) - 1) > 1e-4) {
die sprintf("col %d: sum is not 1 but %f ", $_->{num}, sum(values %$freq));
}
###
# calculate regularised counts (used as pseudo counts)
my $res_count = scalar grep { $freq->{$_} != 0 } keys %$freq;
my $regweight = $GLOB_WEIGHT / $height;
$regweight *= $res_count if $WEIGHTING_MODE eq "blimps";
my %reg = ();
foreach my $aa (@AA_LIST) {
$reg{$aa} =
sum ( map { $freq->{$_} * $regmatrix->{$_}{$aa} / $regmatrix->{"*"}{$_} }
keys %$freq );
}
foreach my $aa (@AA_LIST) {
$freq->{$aa} += $regweight * $reg{$aa};
$freq->{$aa} /= (1 + $regweight);
}
if (defined $MAX_ENTROPY) {
my $entropy=0;
my $total=1;
foreach my $val (values %$freq) {
$entropy -= $val * log($val);
$total -= $val;
}
$entropy /= $LOG20;
if (abs($total) > 1e-4) {
print STDERR "Warning: column $_->{num} does not add up to 1!";
print STDERR "Deviation is $total.\n";
}
push @entropies, $entropy;
}
} # end for each column
# mark entropy based cutoffs
@{$blockref}{"from", "to"} = (0,$blockref->{width});
if (defined $MAX_ENTROPY) {
while ($blockref->{to} - $blockref->{from} >= $MIN_WIDTH) {
if ($entropies[$blockref->{from}]>$MAX_ENTROPY) {
$blockref->{from}++;
} elsif ($entropies[$blockref->{to}-1]>$MAX_ENTROPY) {
$blockref->{to}--;
} else {
last;
}
}
# high-entropy blocks to be removed
if (sum(@entropies[$blockref->{from}..$blockref->{to}-1]) > $MAX_ENTROPY*($blockref->{to}-$blockref->{from})) {
$blockref->{from} = $blockref->{to};
}
}
}
############ main ###############
GetOptions("width=i" => \$MIN_WIDTH,
"qij=s" => \$REG_MATR_FILE,
"mode=s" => \$WEIGHTING_MODE,
"regweight=f" => \$GLOB_WEIGHT,
"max_entropy=f" => \$MAX_ENTROPY,
"min_conserve=f" => \$MIN_CONSERVE,
"noweights" => \$DISABLE_WEIGHTS
);
unless (defined $GLOB_WEIGHT) {
$GLOB_WEIGHT = $DEFAULT_GLOB_WEIGHT;
$GLOB_WEIGHT /= 4 if $WEIGHTING_MODE eq "blimps";
}
if (!defined $MAX_ENTROPY && defined $MIN_CONSERVE) {
$MAX_ENTROPY = 1 - $MIN_CONSERVE;
}
# directories for config files
# this is the method to be used for all AUGUSTUS-PPX scripts
my @CONFIG_DIRS = ("");
if (defined $ENV{"AUGUSTUS_CONFIG_PATH"}) {
push (@CONFIG_DIRS, $ENV{"AUGUSTUS_CONFIG_PATH"}."/profile/");
}
if ($0 =~ /^(.*\/)/ && $1 ne "./") {
push (@CONFIG_DIRS, $1);
}
#
# look for regularisation matrix file
#
unless (defined $REG_MATR_FILE) {
$REG_MATR_FILE="default.qij";
} elsif ($REG_MATR_FILE =~ s/^((~.*?|)\/)//) {
# absolute directory given: do not check other dirs
@CONFIG_DIRS=($1);
}
foreach (@CONFIG_DIRS) {
my $fh;
if (-e "$_$REG_MATR_FILE" && open $fh, "$_$REG_MATR_FILE") {
&read_qij($fh);
last;
}
}
unless (defined $regmatrix) {
print STDERR "Qij file '$REG_MATR_FILE' could not be read.\nCheck the parameter --qij=<filename>.\n\n";
die;
}
#
# read in PRINTS database flat file
#
my $name;
while (<>) {
s/\s*$//;
next unless /^(..)[;] (.*)/;
my ($key, $value) = ($1, $2);
if ($key eq "gc") {
print STDERR "Found new entry '$value'\n";
$name = $value;
$data{$name} = { blocks => [], ID => $name };
} elsif ($key =~ /^g([xt])$/) {
my $out = { "x" => "AC", "t" => "DE" }->{$1};
$data{$name}{$out} = $value;
} elsif ($key =~ /^f/) {
my $blocklist = $data{$name}{blocks};
my $currblock = $blocklist->[-1];
if ($key eq "fc") {
push @$blocklist, {
name => $value,
columns => [],
height => 0
}
} elsif ($key eq "fl") {
$currblock->{width} = $value;
foreach (0..($value-1)) {
push @{$currblock->{columns}}, { str=>[], num=>$_, frq=>{} };
}
} elsif ($key eq "fd") {
my ($motif, $seqname, $pos, $dist) = split /\s+/, $value;
unless (defined $currblock->{width}) {
$currblock->{width} = length($motif);
} elsif (length($motif) != $currblock->{width}) {
die "ERROR: motif width mismatch. Aborting";
}
push @{$currblock->{ibr}}, $dist;
for (my $i=0; $i<$currblock->{width}; $i++) {
my $c = substr($motif, $i, 1);
my $col = $currblock->{columns}[$i];
if (@{$col->{str}} != $currblock->{height}) {
die "ERROR: motif height mismatch. Aborting";
}
push @{$col->{str}}, $c;
$col->{frq}{$c}++;
}
$currblock->{height}++;
}
}
}
foreach (keys %data) {
my $dataset = $data{$_};
my $filename = "$dataset->{AC}.prfl";
open OUTFILE, ">$filename";
my $blocklist = $dataset->{blocks};
my $blcount = 0;
my @ibr = ();
my $ibradd = 0;
print OUTFILE "[name]\n$dataset->{ID}\n";
print OUTFILE "# $dataset->{DE}\n";
foreach my $block (@$blocklist) {
### HERE: define columns and weights (see msa2prfl)
if (@ibr) {
foreach (0..$#ibr) {
$ibr[$_] += $block->{ibr}[$_];
}
} else {
@ibr = @{$block->{ibr}};
}
&calculate_pssm($block);
my ($minprev, $maxprev);
$minprev = $maxprev = $ibr[0];
foreach (@ibr) {
if ($minprev > $_) {
$minprev = $_;
} elsif ($maxprev < $_) {
$maxprev = $_;
}
}
if ($minprev < -$block->{from}) {
$block->{from}=-$minprev;
}
if ($block->{to} - $block->{from} < $MIN_WIDTH) {
$ibradd += $block->{width};
next;
}
$_ += $block->{from} + $ibradd foreach ($minprev, $maxprev);
$ibradd = $block->{width}-$block->{to};
@ibr=();
print OUTFILE "\n[dist]\n# distance from previous block\n";
print OUTFILE "# <min> <max>\n";
print OUTFILE "$minprev\t$maxprev\n\n";
print OUTFILE "[block]\n# block no. $blcount follows, $block->{height} sequences, length $block->{width}\nname=$block->{name}\n";
print OUTFILE "# note: PSSM column 0 corresponds to original block column $block->{from}\n" if $block->{from}>0;
$blcount++;
print OUTFILE "#\n# <colnr> <probs for $AMINO_ACIDS>\n";
print OUTFILE "#\t".join("\t", @AA_LIST)."\n";
for (my $colno = $block->{from}; $colno < $block->{to}; $colno++) {
my $freq = $block->{columns}[$colno]{frq};
print OUTFILE "".($colno-$block->{from})."\t".join("\t", map { sprintf(($_ < 1e-4 ? "%.2g" : "%7.5f"), $_) } @{$freq}{@AA_LIST})."\n";
}
}
print OUTFILE "\n# created by:\n";
print OUTFILE "# $0 $INITARGS\n";
close OUTFILE;
print "Wrote '$filename'.\n";
}
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