#!/usr/bin/perl
# blast2map.pl
my $novote= 0; # simple page for viewing
=item result from dgg
Method Score
DGIL_SNP 74
NCBI_GNO 32
EISE_CGM 10
OXFD_GPI 2
PACH_GMP 0
FlyGeneHSP 20
erecta_Acp100=15
yakuba_Acp133=20
yakuba_Acp134=24
yakuba_Acp157=13
yakuba_Acp157a=13
yakuba_Acp158=0
yakuba_Acp223=7
yakuba_Acp224=9
yakuba_Acp225=35
yakuba_Gene144=2
=cut
my $footer= <<'EOF';
New gene dyak-acps-begun.fasta
and Source data, code for this table
Don Gilbert, may 06
my results:
Method Score
DGIL_SNP 74
NCBI_GNO 32
EISE_CGM 10
OXFD_GPI 2
PACH_GMP 0
FlyGeneHSP 20
EOF
my $header = <<"EOF";
Drosophila gene prediction assessment
How well do gene predictors find new genes found by other methods?
Recently Evolved Genes Identified From Drosophila yakuba and D. erecta
Accessory Gland Expressed Sequence Tags
EOF
if($novote) {
$header .= << "EOF";
Use the web links in the "match link" column to view annotations at the
site of these BLAST-located coding sequence of new genes.
Score the gene predictions here .
EOF
} else {
$header .= << "EOF";
Assessment: Eye-ball method.
Use the web links in the "match link" column to view annotations at the
site of these BLAST-located coding sequence of new genes.
To score annotations, choose for each annotation method
how well it finds the new gene.
Scores are (5) exon overlap, (2) exon within 1kb, (1)
exon within 2kb, only where exon doesn't belong to other well-known gene.
Clicking the Submit button will e-mail your scoring to drospege.
No match
Overlaps
Exon 1kb
Exon 2kb
";
print "
\n";
print $header;
unless($novote) {
print '\n" unless($novote);
print $footer;
print "\n";
sub amin {
my($a,$b)= @_;
$a= abs($a); $b= abs($b);
return ($a < $b) ? $a : $b;
}
sub nearby {
my($sb,$se,$lb,$le)= @_;
my $dist= amin($sb - $le, $se - $lb);
##warn "nearby($sb,$se,$lb,$le) = $dist\n";
return ($dist <= $MAX_EXON_DIST);
}
sub printHsp {
my($sid, $qid, $hsp,$hspid)= @_;
my($sorg,$schr)= split(/[:|]/, $sid,2);
$sorg =~ s/_.*$//;
my($bstart,$bend,$bstrand);
my $bits= 0;
foreach my $p (@$hsp) {
my($xqid, $xsid, $s_start, $s_end, $s_strand, $bit_score)= @$p;
$bits += $bit_score;
$bstrand= $s_strand;
$bstart= $s_start if($bstart==0 || $bstart>$s_start);
$bend= $s_end if($bend < $s_end);
}
return unless($bend);
return if ($bits < $MIN_BITSCORE);
my $gurl= gbrowseFromOrgChrStartStop($sorg, $schr, $bstart, $bend, $bstrand, $qid, $hsp);
my $hmap = " $sid ";
(my $hgff = $gurl) =~ s/;add=.*$//;
$hgff = " GFF ";
my @predvals= map {
my $pgid=join("_",$_,$qid,$hspid);
(my $v= $predval) =~ s/GENEID_GRPID/$pgid/;
$v; } @preds;
@predvals=() if ($novote);
#print join("\t", $qid, $bit_score, $sid, $gurl), "\n";
print "",join(" ", $qid, $bits, "$hmap .. $hgff", @predvals),
"