my $self = shift;
my $source = $self->source();
my $target = $self->target();
my $dbh = $self->dbh();
$self->debug("AnophelesGambiae Specific: building prediction_exon table");
#
# In Anopheles the predicion transcripts were computed in chromosomal
# coords, so convert them to chromosomal coords and merge any adjacent
# exons
#
my $sql =
"SELECT pt.prediction_transcript_id, tcm.new_id as seq_region_id, " .
" IF(a.contig_ori=1,(pt.contig_start+a.chr_start-a.contig_start),".
" (a.chr_start+a.contig_end-pt.contig_end)) as start, " .
" IF(a.contig_ori=1,(pt.contig_end+a.chr_start-a.contig_start)," .
" (a.chr_start+a.contig_end-pt.contig_start)) as end, " .
" a.contig_ori * pt.contig_strand as strand, " .
" pt.start_phase, pt.score, pt.p_value " .
"FROM $source.assembly a, $target.tmp_chr_map tcm, " .
" $source.prediction_transcript pt " .
"WHERE pt.contig_id = a.contig_id " .
"AND a.chromosome_id = tcm.old_id " .
"ORDER BY pt.prediction_transcript_id, exon_rank";
my $sth = $dbh->prepare($sql);
$sth->execute();
my $prev_end = undef;
my $prev_start = undef;
my $prev_id = undef;
my $rank = undef;
my %prev_exon = ();
while(my $row = $sth->fetchrow_arrayref()) {
my ($pt_id, $sr_id, $sr_start, $sr_end, $sr_strand, $start_phase,
$score, $p_value) = @$row;
if(defined($prev_id) && ($prev_id == $pt_id)) {
#still in the same transcript
if($sr_strand == 1 &&
defined($prev_end) && $prev_end == $sr_start-1) {
$self->debug("merged exon $rank in prediction_transcript $pt_id\n");
#adjacent exons forward strand - merge them
$prev_exon{'seq_region_end'} = $sr_end;
$prev_end = $sr_end;
} elsif($sr_strand == -1 &&
defined($prev_start) && $prev_start == $sr_end+1) {
$self->debug("merged exon $rank in prediction_transcript $pt_id\n");
#adjacent exons negative strand - merge them
$prev_exon{'seq_region_start'} = $sr_start;
$prev_start = $sr_start;
} else {
#non-adjacent exons in the same transcript - no merge
$rank++;
#store the previous exon
$self->store_pexon(\%prev_exon);
#make current exon the previous exon
%prev_exon = ('prediction_transcript_id' => $pt_id,
'seq_region_id' => $sr_id,
'seq_region_start' => $sr_start,
'seq_region_end' => $sr_end,
'seq_region_strand' => $sr_strand,
'start_phase' => $start_phase,
'score' => $score,
'p_value' => $p_value,
'rank' => $rank);
}
} else {
#store previous exon
$self->store_pexon(\%prev_exon) if(%prev_exon);
#new ptranscript
$rank = 1;
$prev_id = $pt_id;
$prev_end = $sr_end;
$prev_start = $sr_start;
%prev_exon = ('prediction_transcript_id' => $pt_id,
'seq_region_id' => $sr_id,
'seq_region_start' => $sr_start,
'seq_region_end' => $sr_end,
'seq_region_strand' => $sr_strand,
'start_phase' => $start_phase,
'score' => $score,
'p_value' => $p_value,
'rank' => $rank);
}
}
#store the very last exon in the table
$self->store_pexon(\%prev_exon) if(%prev_exon);
$sth->finish();
$self->debug("AnophelesGambiae Specific: building prediction_transcript " .
"table");
$dbh->do
("INSERT INTO $target.prediction_transcript (prediction_transcript_id, " .
" seq_region_id, seq_region_start, seq_region_end, " .
" seq_region_strand, analysis_id ) " .
"SELECT pt.prediction_transcript_id, tcm.new_id as seq_region_id, " .
" MIN(IF(a.contig_ori=1,(pt.contig_start+a.chr_start-a.contig_start),".
" (a.chr_start+a.contig_end-pt.contig_end))) as start, " .
" MAX(IF(a.contig_ori=1,(pt.contig_end+a.chr_start-a.contig_start)," .
" (a.chr_start+a.contig_end-pt.contig_start))) as end, " .
" a.contig_ori * pt.contig_strand as strand, " .
" pt.analysis_id " .
"FROM $source.assembly a, $target.tmp_chr_map tcm, " .
" $source.prediction_transcript pt " .
"WHERE pt.contig_id = a.contig_id " .
"AND a.chromosome_id = tcm.old_id " .
"GROUP BY prediction_transcript_id");
return;
}
Code:
