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#!/usr/bin/perl
#
# wig2hints.pl
#
# convert a file with conservation scores in wiggle format to a file with
# CDSpart hints for AUGUSTUS
#
# Mario Stanke 4.7.2007
use strict;
use Getopt::Long;
if( grep /^--?h$/, @ARGV ) {
exec("perldoc $0");
}
my $source = "w2h";
my $strand = ".";
my $type = "CDSpart";
my $src = "X";
my $pri;
my $oldseqname = "";
my $width = 40;
my $margin = 20;
my $radius = 0;
my $minscore = 0.4;
my $minthresh = 0.4;
my $maxchunksize = 1100000; # to save memory
my $minchunksize = 1000000; #
my $offset = 0;
my $av;
my $prune = 0;
my $step = 1;
my $UCSC = "";
my $rn = 0; # running number to make group field unique for ucsc browser
my ($seqname, $offset, $v);
my @values = ();
GetOptions('width:i'=>\$width,
'radius:f'=>\$radius,
'margin:i'=>\$margin,
'minscore:f'=>\$minscore,
'minthresh:f'=>\$minthresh,
'type:s'=>\$type,
'prune:f'=>\$prune,
'pri:i'=>\$pri,
'strand:s'=>\$strand,
'UCSC:s'=>\$UCSC,
'src:s'=>\$src);
if ($UCSC ne ""){
open (TRACK, ">$UCSC") or die ("Could not open file $UCSC for writing.");
}
while (<STDIN>) {
if (/fixedStep chrom=(\S+)\s+start=(\d+) step=(\d+)/) {
$seqname = $1;
$offset = $2;
$step = $3;
if ($seqname ne $oldseqname && $oldseqname ne "") {
printScores();
$offset = 0;
}
$oldseqname = $seqname;
} elsif (/variableStep chrom=(\S+)/){
$seqname = $1;
if ($seqname ne $oldseqname && $oldseqname ne "") {
printScores();
$offset = 0;
}
$oldseqname = $seqname;
} elsif (/^([\.0-9]+)$/){
$v = $1;
for (my $i=0; $i<$step; $i++) {
$values[$offset+$i] = $v;
}
$offset += $step;
} elsif (/^(\d+)\s*([\.0-9]+)$/){
$values[$1] = $2;
if (($2 < $minthresh && $1 > $offset + $minchunksize) || ($1 > $offset + $maxchunksize)){
printScores();
}
}
}
printScores();
sub printScores {
my ($a, $b, $aprime, $bprime) = ($offset,0,0,0);
my $m;
while ($a < @values) {
while ($a<@values && $values[$a] < $minthresh){
$a++;
}
$b=$a;
while ($b<@values && $values[$b] >= $minthresh) {
$b++;
}
$b--;
# [a,b] is contiguous island above minthresh now
#
# --------------------------------------------------------------------------------------------
# a b
# | margin |rest| width | width | width | width | width |rest| margin |
# hints | | | | |
# print "a=$a, b=$b\n";
$aprime = $a + $margin;
$bprime = $b - $margin;
if ($aprime>$bprime) {
$aprime=$bprime=int(($aprime+$bprime)/2);
}
#
# big exon "mountains" often have a "foot" area
# these two lines are trying to remove it, if $prune is >0
#
$av = 0;
for (my $j=$aprime; $j<=$bprime; $j++){
$av += $values[$j];
}
$av /= ($bprime-$aprime+1);
while ($prune && $prune * $av > $values[$aprime] && $aprime < $bprime) { $aprime++;}
while ($prune && $prune * $av > $values[$bprime] && $aprime < $bprime) { $bprime--;}
my $len = $bprime-$aprime+1;
my $n = int($len/$width);
$n=1 if ($n<1);
for (my $i=0; $i<$n; $i++) {
$m = int($aprime+($len - ($n-1)*$width)/2+$i*$width+0.5);
$av = 0;
for (my $j=0; $j<$width; $j++){
$av += $values[$m+$j-int($width/2)];
}
$av = sprintf("%.3f", $av / $width);
if ($av > $minscore) {
my ($from, $to) = (int($m-$radius+0.5), int($m+$radius+0.5));
print "$oldseqname\t$source\t$type\t$from\t$to\t$av\t$strand\t.\t";
print "src=$src;";
print "pri=$pri;" if (defined($pri));
print "mult=" . int($av) . ";\n";
print TRACK "$oldseqname\t$source\t$type\t$from\t$to\t$av\t$strand\t.\t$av $m " . ++$rn . "\n" if ($UCSC ne "");
}
}
$a = $b+1;
}
$offset = $a;
@values = ();
}
close TRACK if ($UCSC ne "");
__END__
=head1 NAME
wig2hints -- convert a file with conservation scores in wiggle format to a file with
CDSpart/exonpart hints for AUGUSTUS
=head1 SYNOPSIS
wig2hints.pl < score.wig > hints.gff
score.wig - a file in wiggle format, e.g.
fixedStep chrom=Nt-gDNA_Contig1538203 start=829 step=1
0.084
0.111
0.267
0.471
...
fixedStep chrom=Nt-gDNA_Contig1538203 start=873 step=1
0.048
0.102
0.128
...
=head1 OPTIONS
--width=n Default: 40
--margin=n Default: 20
--minthresh=p Default: 0.4 horizontal cutoff for determining intervals
--minscore=p Default: 0.4 consider only intervals with an average score at least this high
--type=s Default: print this in the third column (default:"CDSpart")
--pri=n print priority n in last column
--radius=n length of hint interval is 2*radius+1
--strand=s Default: "." print this in the strand column
--prune=f Default: 0 (off). Remove boundary areas that have coverage less than f*100% of the average over the island
--src=s Default: "X" print src=s in the last column
--UCSC=s Filename for track of UCSC genome browser custom track
=head1 DESCRIPTION
=cut
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