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Commit 4b02ab17 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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No functional changes, apart from reporting the number of exons scores 

falling below the threshold in the similarity scoring step specifically
due to the source and target exons being on two different seq_regions.
parent c8620d63
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modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
+ 73
− 52
View file @ 4b02ab17
......@@ -72,7 +72,8 @@ sub score_exons {
$self->logger->info( "\nMerging scoring matrices...\n",
0, 'stamped' );
$matrix->merge($exonerate_matrix);
} else {
}
else {
$self->logger->info("\nOverlap scoring matrix:\n");
$self->log_matrix_stats($matrix);
}
......@@ -100,32 +101,38 @@ sub score_exons {
sub overlap_score {
my $self = shift;
my $dump_path = path_append($self->conf->param('basedir'), 'matrix');
my $matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
-DUMP_PATH => $dump_path,
-CACHE_FILE => 'exon_overlap_matrix.ser',
);
my $dump_path =
path_append( $self->conf->param('basedir'), 'matrix' );
my $matrix =
Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
-DUMP_PATH => $dump_path,
-CACHE_FILE => 'exon_overlap_matrix.ser',
);
my $overlap_cache = $matrix->cache_file;
if (-s $overlap_cache) {
if ( -s $overlap_cache ) {
# read from file
$self->logger->info("Reading exon overlap scoring matrix from file...\n", 0, 'stamped');
$self->logger->debug("Cache file $overlap_cache.\n", 1);
$self->logger->info(
"Reading exon overlap scoring matrix from file...\n",
0, 'stamped' );
$self->logger->debug( "Cache file $overlap_cache.\n", 1 );
$matrix->read_from_file;
$self->logger->info("Done.\n", 0, 'stamped');
} else {
$self->logger->info( "Done.\n", 0, 'stamped' );
}
else {
# build scoring matrix
$self->logger->info("No exon overlap scoring matrix found. Will build new one.\n");
$self->logger->info(
"No exon overlap scoring matrix found. Will build new one.\n");
if ($self->cache->highest_common_cs) {
$self->logger->info("Overlap scoring...\n", 0, 'stamped');
if ( $self->cache->highest_common_cs ) {
$self->logger->info( "Overlap scoring...\n", 0, 'stamped' );
$matrix = $self->build_overlap_scores($matrix);
$self->logger->info("Done.\n", 0, 'stamped');
$self->logger->info( "Done.\n", 0, 'stamped' );
}
# write scoring matrix to file
......@@ -134,42 +141,48 @@ sub overlap_score {
}
return $matrix;
}
} ## end sub overlap_score
#
# map the remaining exons using exonerate
#
sub exonerate_score {
my $self = shift;
my $self = shift;
my $matrix = shift;
unless ($matrix and
$matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
unless ( $matrix and
$matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix') )
{
throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
}
my $dump_path = path_append($self->conf->param('basedir'), 'matrix');
my $dump_path =
path_append( $self->conf->param('basedir'), 'matrix' );
my $exonerate_matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
-DUMP_PATH => $dump_path,
-CACHE_FILE => 'exon_exonerate_matrix.ser',
);
my $exonerate_matrix =
Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
-DUMP_PATH => $dump_path,
-CACHE_FILE => 'exon_exonerate_matrix.ser',
);
my $exonerate_cache = $exonerate_matrix->cache_file;
if (-s $exonerate_cache) {
if ( -s $exonerate_cache ) {
# read from file
$self->logger->info("Reading exonerate matrix from file...\n", 0, 'stamped');
$self->logger->debug("Cache file $exonerate_cache.\n", 1);
$self->logger->info( "Reading exonerate matrix from file...\n",
0, 'stamped' );
$self->logger->debug( "Cache file $exonerate_cache.\n", 1 );
$exonerate_matrix->read_from_file;
$self->logger->info("Done.\n", 0, 'stamped');
$self->logger->info( "Done.\n", 0, 'stamped' );
} else {
}
else {
# build scoring matrix
$self->logger->info("No exonerate matrix found. Will build new one.\n");
$self->logger->info(
"No exonerate matrix found. Will build new one.\n");
# dump exons to fasta files
my $dump_count = $self->dump_filtered_exons($matrix);
......@@ -177,23 +190,25 @@ sub exonerate_score {
if ($dump_count) {
# run exonerate
$self->run_exonerate;
# parse results
$self->parse_exonerate_results($exonerate_matrix);
} else {
}
else {
$self->logger->info("No source and/or target exons dumped, so don't need to run exonerate.\n");
$self->logger->info( "No source and/or target exons dumped, " .
"so don't need to run exonerate.\n" );
}
# write scoring matrix to file
$exonerate_matrix->write_to_file;
}
} ## end else [ if ( -s $exonerate_cache)]
return $exonerate_matrix;
}
} ## end sub exonerate_score
#
# Algorithm:
......@@ -281,7 +296,7 @@ sub build_overlap_scores {
$self->calc_overlap_score( $source_ec->[0], $target_exon,
$matrix );
}
}
} ## end else [ if ( $source_overlap{ ...})]
# get next source exon container
$source_ec = shift(@source_exons);
......@@ -639,12 +654,12 @@ sub write_filtered_exons {
return $dumped_exons;
}
sub parse_exonerate_results {
my ( $self, $exonerate_matrix ) = @_;
unless ( $exonerate_matrix
and $exonerate_matrix->isa(
unless ( defined($exonerate_matrix)
&&
$exonerate_matrix->isa(
'Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')
)
{
......@@ -658,10 +673,11 @@ sub parse_exonerate_results {
my $num_files = 0;
my $num_lines = 0;
opendir( DUMPDIR, $dump_path )
or $self->logger->error("Can't open $dump_path for reading: $!");
opendir( DUMPDIR, $dump_path ) or
$self->logger->error("Can't open $dump_path for reading: $!");
my $penalised = 0;
my $killed = 0;
while ( defined( my $file = readdir(DUMPDIR) ) ) {
unless ( $file =~ /exonerate_map\.\d+/ ) { next }
......@@ -676,8 +692,8 @@ sub parse_exonerate_results {
$num_lines++;
chomp;
# line format:
# myinfo: source_id target_id match_length source_length target_length
# line format:
# myinfo: source_id target_id match_length source_length target_length
my ( undef, $source_id, $target_id, $match_length, $source_length,
$target_length )
= split;
......@@ -687,7 +703,8 @@ sub parse_exonerate_results {
if ( $source_length == 0 or $target_length == 0 ) {
$self->logger->warning(
"Alignment length is 0 for $source_id or $target_id.\n");
} else {
}
else {
$score = 2*$match_length/( $source_length + $target_length );
}
......@@ -714,7 +731,10 @@ sub parse_exonerate_results {
$exonerate_matrix->add_score( $source_id, $target_id,
$score );
}
}
else {
++$killed;
}
} ## end if ( $score > $threshold)
} ## end while (<F>)
......@@ -726,8 +746,9 @@ sub parse_exonerate_results {
$self->logger->info(
"Done parsing $num_lines lines from $num_files result files.\n",
0, 'stamped' );
$self->logger->info( "Penalised $penalised exon alignments "
. "for not being on the same seq_region.\n",
$self->logger->info( "Penalised $penalised exon alignments " .
"for not being on the same seq_region " .
"($killed killed).\n",
0,
'stamped' );
......
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