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#!/usr/bin/perl -w
################################################################################
#
# Project: Gene Prediction with Protein Family Patterns
# Author: Oliver Keller
# Date: 2010-07-07
# Version: accompanying Scipio 1.4
#
#
# yaml2gff.pl
#
#
# This script transforms the yaml output of scipio into easily readable GFF
#
# The output produces is conforming to the GFF3 standard; however the term "Target" used
# in GFF3 is replaced by "Query".
# In the context of Scipio, the "target" sequence is the referenced genomic sequence while the
# "query" is the aligned protein sequence. In other contexts (as in the GFF standard too), the
# "target" sequence is what Scipio is referring to as the "query". To avoid confusion, in the
# GFF produces by yaml2gff the term "target" is omitted completely.
#
# the protein sequence shown contains only matched amino acids, together with the following
# extra symbols:
# "." for an unmatched amino acid in the query (gaps, case 5)
# "x" for a mismatch / undetermined amino acid (cases 1-3, 10-13, 15, 16)
# "-" for an extra codon (or pair or single nucleotide) in the target (cases 4, 6-9, 17)
# "*" for a matched stop codon (case 14)
#
# Counting of bps/aas: is transforming coordinates from YAML file (see usage.html)
# into low-high coordinates according to GFF standard
#
use strict;
use List::Util('sum', 'max');
use YAML;
use Getopt::Long;
my $PROT_WIDTH=98;
my $DNA_ORDER=0;
my $QPFX="prot";
my $TPFX="dna";
my $TRPFX="trans";
my $QNPFX="nucl";
my $filterStatus; # filter this status out
my $help=0; # whether to print usage information
my %PARAMETER = ("filterstatus:s" => \$filterStatus,
"help!" => \$help);
sub usage
{
print STDERR "
usage:
yaml2gff.pl [<options>] < scipio.yaml > scipio.gff
Options: --help print this help message
--filterstatus=<value> filter out alignments with given status, e.g. 'incomplete'
";
exit 1;
}
sub nu_to_aa {
my $arg = shift;
my $residue = ($arg+1) % 3 -1; # -1, 0, 1
return ($arg-$residue)/3;
}
sub escape {
foreach(@_) {
s/([^a-zA-Z0-9.:^*$@!+_?-|])/sprintf("%%%02X",ord($1))/ge;
}
}
sub with_number {
my ($n, $s, $alt) = @_;
$alt = "${s}s" unless (defined $alt);
return ($n==1) ? "$n$s" : "$n$alt";
}
sub get_gapstr {
my ($frameshifts, $qfrom, $qto) = @_;
return "" unless(defined $frameshifts && @$frameshifts);
my $result="";
my @matches = map { &nu_to_aa($_->{"${QNPFX}_start"}) } @$frameshifts;
$matches[0] -= $qfrom;
push @matches, $qto;
for my $i (1..@$frameshifts) {
$matches[$i] -= &nu_to_aa($frameshifts->[$i-1]{"${QNPFX}_end"});
}
foreach (@$frameshifts) {
my $base_count = ($_->{"${TPFX}_end"}) - ($_->{"${TPFX}_start"});
my $aa_count = (($_->{"${QNPFX}_end"}) - ($_->{"${QNPFX}_start"})) / 3;
$result.="M".(shift @matches)." ";
if ($aa_count == 0) {
my $fs = $base_count % 3;
$base_count -= $fs;
my $deletes = $base_count / 3;
$result.="D$deletes " if ($deletes);
$result.="F$fs " if ($fs);
} else {
$result.="I$aa_count ";
$result.="F$base_count " if ($base_count);
}
}
return ";Gap=${result}M$matches[0]";
}
sub output {
my ($queryname, $hitlist) = @_;
next if ($filterStatus && $hitlist->[0]{"status"} eq $filterStatus);
escape($queryname);
print "##query\t$queryname 1 ".$hitlist->[0]{"${QPFX}_len"};
my ($pstart, $pend, $plen) = ($hitlist->[0]{"${QPFX}_start"}, @{$hitlist->[-1]}{"${QPFX}_end", "${QPFX}_len"});
my $prev_end = 0;
my $matched_prot = "." x $plen;
my @minuses = ();
foreach my $hitref (@$hitlist) {
my ($hit_id, $matchings, $strand, $targetname, $score,
$gapcount, $stopcodon, $status, $protseq,
$querystart, $queryend, $total_length) =
@$hitref{"ID", "matchings", "strand", "target", "score",
"gaps", "stopcodon", "status", "${QPFX}_seq",
"${QPFX}_start", "${QPFX}_end", "${QPFX}_len"};
$targetname =~ s/\s.*//;
escape($targetname);
$gapcount = 0 unless (defined $gapcount);
$stopcodon = "" unless (defined $stopcodon);
if ($strand eq "-" || $strand =~ /minus/ || $strand =~ /back/) {
$strand = "-";
} elsif ($strand eq "+" || $strand =~ /plus/ || $strand =~ /forward/) {
$strand = "+";
} else {
my $dnapos = $hitref->{"${TPFX}_start"};
$dnapos = $hitref->{matchings}[0]{"${TPFX}_start"} unless defined $dnapos;
if (defined $dnapos) {
$strand = $dnapos < 0 ? "-" : "+";
} else {
$strand = ".";
}
}
my $complement = $strand eq "-";
my @exons = grep { $_->{type} eq "exon" } @$matchings;
my @mismatchcounts = map { scalar @{$_->{mismatchlist}} } @exons;
my @undeterminedcounts = map { scalar @{$_->{undeterminedlist}} } @exons;
my $total_mismatches = sum(@mismatchcounts,@undeterminedcounts,0);
$querystart=0 unless (defined $querystart);
$queryend=$total_length unless (defined $queryend);
if (defined $protseq) {
substr($matched_prot, $querystart, $queryend-$querystart) = $protseq;
}
if ($prev_end < $querystart) {
print "\n# gap ".($prev_end+1)." $querystart";
}
my $matchsize = $queryend-$querystart;
my $matchcount = $matchsize - $gapcount - $total_mismatches;
my $has_bad_introns =
grep ({ /intron\?/ } map { $_->{type} } @$matchings);
my @gff_lines = ();
foreach (@$matchings) {
my ($type, $qnfrom,$qnto) = @$_{"type", "${QNPFX}_start","${QNPFX}_end"};
if ($type eq "exon") {
my ($qfrom, $qto) = map { &nu_to_aa($_); } ($qnfrom, $qnto);
my ($frameshifts,$mismatches,$undetermined,$addprotseq, $trans,
$tfrom, $tto)
= @$_{"seqshifts","mismatchlist","undeterminedlist","${QPFX}_seq","translation",
"${TPFX}_start", "${TPFX}_end"};
if (defined $addprotseq) {
substr($matched_prot, $qfrom, $qto-$qfrom)=$addprotseq;
}
my ($first, $last) = $complement? (-$tto+1, -$tfrom+0) : ($tfrom+1, $tto+0);
my @xpos = sort { $a <=> $b } (@$mismatches,@$undetermined);
my $misstr = (@xpos)? ";Mismatches=".join(" ", @xpos) : "";
map { substr($matched_prot,$_-1,1)="x"; } @xpos;
my $gapstr = &get_gapstr($frameshifts, $qfrom, $qto);
foreach (@$frameshifts) {
my ($fsstart, $fsend) = map { &nu_to_aa($_) } @{$_}{"${QNPFX}_start", "${QNPFX}_end"};
my $excount = int(($_->{"${TPFX}_end"} - $_->{"${TPFX}_start"} + 2) / 3);
if ($fsend > $fsstart) {
substr($matched_prot, $fsstart, $fsend-$fsstart) = ("x" x $excount).("." x ($fsend-$fsstart-$excount));
} else {
push @minuses, ($fsstart) x $excount;
}
}
push (@gff_lines,
"$targetname\tScipio\tprotein_match\t$first\t$last\t$score\t$strand\t".
(-$qnfrom % 3)."\tID=$hit_id;Query=$queryname ".($qfrom+1).
" $qto$misstr$gapstr");
} elsif ($type eq "gap") {
my ($qfrom, $qto) = map { &nu_to_aa($_) } ($qnfrom, $qnto);
substr($matched_prot, $qfrom, $qto-$qfrom) = "." x ($qto-$qfrom);
push @gff_lines, "# gap ".($qfrom+1)." $qto";
}
}
@gff_lines = reverse @gff_lines if ($complement && $DNA_ORDER);
print "\n".join("\n", @gff_lines);
$prev_end = $queryend;
}
if (defined $pend && $pend < $plen) {
print "\n# gap ".($pend+1)." $plen";
}
foreach (reverse @minuses) {
substr($matched_prot, $_, 0) = "-";
}
$matched_prot = "protein sequence = [$matched_prot";
do {
print "\n# ".substr($matched_prot,0,$PROT_WIDTH,"");
} while ($matched_prot);
print "]\n#\n";
}
### Command Line
&GetOptions (%PARAMETER) or &usage;
&usage if ($help);
my @input = split("\n---",join("",<>));
shift @input if (@input && $input[0]!~/^---/);
print "##gff-version\t3\n";
print STDERR "Found ".&with_number(scalar @input, " YAML entry", " YAML entries").".\n";
foreach (@input) {
s/^(---)?/---/;
s/$/\n/;
my $hits = YAML::Load($_);
print STDERR "[";
foreach (sort { $a cmp $b } keys %$hits) {
&output($_, $hits->{$_});
print STDERR " $_ ";
}
print STDERR "]\n";
}
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