From 4603dc5b81af06b7cbffb6ee108b9343cb81350d Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Fri, 29 Jun 2007 14:35:43 +0000
Subject: [PATCH] latest state of the code (bugfixes and adaptations due to
changes in ConfParser and Logger)
---
modules/Bio/EnsEMBL/IdMapping/Cache.pm | 66 +++++----
.../Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm | 140 +++++++++---------
.../Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm | 60 ++++----
modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm | 8 +-
.../EnsEMBL/IdMapping/ScoredMappingMatrix.pm | 21 ++-
.../IdMapping/TranscriptScoreBuilder.pm | 53 +++----
6 files changed, 188 insertions(+), 160 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/Cache.pm b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
index d4e8234161..2162d943a0 100644
--- a/modules/Bio/EnsEMBL/IdMapping/Cache.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
@@ -47,6 +47,10 @@ use Storable qw(nfreeze thaw nstore retrieve);
# define available cache names here
my @cache_names = qw(
exons_by_id
+ transcripts_by_id
+ transcripts_by_exon_id
+ genes_by_id
+ genes_by_transcript_id
);
@@ -101,12 +105,17 @@ sub build_cache {
my $i = scalar(@$genes);
# find common coord_system
- $self->find_common_coord_systems;
+ my $common_cs_found = $self->find_common_coord_systems;
- # find out whether native and common coord_system are identical
+ # find out whether native coord_system is a common coord_system.
+ # if so, you don't need to project.
+ # also don't project if no common coord_system present
my $need_project = 1;
- my $csid = join(':', $slice->coord_system_name, $slice->coord_system->version);
- $need_project = 0 if ($self->is_common_cs($csid));
+ my $csid = join(':', $slice->coord_system_name,
+ $slice->coord_system->version);
+ if ($self->is_common_cs($csid) or !$self->highest_common_cs) {
+ $need_project = 0;
+ }
# build cache
my $type = "$dbtype.$slice_name";
@@ -163,8 +172,8 @@ sub build_cache_from_genes {
]);
# build gene caches
- #$self->add($type, 'genes_by_id', $gene->dbID, $lgene);
- #$self->add($type, 'genes_by_stable_id', $gene->stable_id, $lgene);
+ $self->add('genes_by_id', $type, $gene->dbID, $lgene);
+ #$self->add('genes_by_stable_id', $type, $gene->stable_id, $lgene);
# transcripts
foreach my $tr (@{ $gene->get_all_Transcripts }) {
@@ -180,9 +189,9 @@ sub build_cache_from_genes {
#$lgene->add_Transcript($ltr);
# build transcript caches
- $self->add($type, 'transcripts_by_id', $tr->dbID, $ltr);
- #$self->add($type, 'transcripts_by_stable_id', $tr->stable_id, $ltr);
- $self->add($type, 'genes_by_transcript_id', $tr->dbID, $lgene);
+ $self->add('transcripts_by_id', $type, $tr->dbID, $ltr);
+ #$self->add('transcripts_by_stable_id', $type, $tr->stable_id, $ltr);
+ $self->add('genes_by_transcript_id', $type, $tr->dbID, $lgene);
# translation (if there is one)
if (my $tl = $tr->translation) {
@@ -193,9 +202,9 @@ sub build_cache_from_genes {
#$ltr->add_Translation($ltl);
- #$self->add($type, 'translations_by_id', $tl->dbID, $ltl);
- #$self->add($type, 'translations_by_stable_id', $tl->stable_id, $ltl);
- #$self->add($type, 'translations_by_transcript_id', $tr->dbID, $ltl);
+ #$self->add('translations_by_id', $type, $tl->dbID, $ltl);
+ #$self->add('translations_by_stable_id', $type, $tl->stable_id, $ltl);
+ #$self->add('translations_by_transcript_id', $type, $tr->dbID, $ltl);
undef $tl;
}
@@ -233,8 +242,8 @@ sub build_cache_from_genes {
$ltr->add_Exon($lexon);
$self->add('exons_by_id', $type, $exon->dbID, $lexon);
- #$self->add($type, 'genes_by_exon_id', $exon->dbID, $lgene);
- $self->add_list($type, 'transcripts_by_exon_id', $exon->dbID, $ltr);
+ #$self->add('genes_by_exon_id', $type, $exon->dbID, $lgene);
+ $self->add_list('transcripts_by_exon_id', $type, $exon->dbID, $ltr);
undef $exon;
}
@@ -295,7 +304,7 @@ sub get_by_key {
# transparently load cache from file unless already loaded
unless ($self->{'instance'}->{'loaded'}->{"$name:$type"}) {
- $self->load_and_merge($name, $type);
+ $self->read_and_merge($name, $type);
}
return $self->{'cache'}->{$name}->{$type}->{$key};
@@ -311,7 +320,7 @@ sub get_by_name {
# transparently load cache from file unless already loaded
unless ($self->{'instance'}->{'loaded'}->{"$name:$type"}) {
- $self->load_and_merge($name, $type);
+ $self->read_and_merge($name, $type);
}
return $self->{'cache'}->{$name}->{$type} || {};
@@ -328,7 +337,7 @@ sub get_count_by_name {
# transparently load cache from file unless already loaded
unless ($self->{'instance'}->{'loaded'}->{"$name:$type"}) {
- $self->load_and_merge($name, $type);
+ $self->read_and_merge($name, $type);
}
return scalar(keys %{ $self->get_by_name($name, $type) });
@@ -382,6 +391,7 @@ sub find_common_coord_systems {
}
}
+ return $found_highest;
}
@@ -427,7 +437,7 @@ sub seq_regions_compatible {
if ($equal/$s_count > 0.5 and $equal/$t_count > 0.5) {
return(1);
} else {
- $self->logger->log("Only $equal seq_regions identical for ".$cs->name." ".$cs->version."\n");
+ $self->logger->info("Only $equal seq_regions identical for ".$cs->name." ".$cs->version."\n");
return(0);
}
@@ -491,10 +501,10 @@ sub cache_file_exists {
my $cache_file = $self->cache_file($name, $type);
if (-s $cache_file) {
- $self->logger->log("Cache file found. Will read from $cache_file.\n", 3);
+ $self->logger->info("Cache file found. Will read from $cache_file.\n", 3);
return 1;
} else {
- $self->logger->log("No cache file found. Will build cache from db.\n", 3);
+ $self->logger->info("No cache file found for $name/$type. Will build cache from db.\n", 3);
return 0;
}
}
@@ -573,7 +583,7 @@ sub write_to_file {
throw("You must provide a cache type.") unless $type;
unless ($self->{'cache'}->{$name}->{$type}) {
- $self->logger->log_warning("No features found in $name/$type. Won't write cache file.\n");
+ $self->logger->warning("No features found in $name/$type. Won't write cache file.\n");
return;
}
@@ -639,13 +649,13 @@ sub read_from_file {
throw("No valid cache file found at $cache_file.");
}
- #$self->logger->log_stamped("Reading cache from file...\n");
- #$self->logger->log("Cache file $cache_file.\n", 1);
+ #$self->logger->info("Reading cache from file...\n", 0, 'stamped');
+ #$self->logger->info("Cache file $cache_file.\n", 1);
eval { $self->{'cache'}->{$name}->{$type} = retrieve($cache_file); };
if ($@) {
throw("Unable to retrieve cache: $@");
}
- #$self->logger->log_stamped("Done.\n");
+ #$self->logger->info("Done.\n", 0, 'stamped');
return $self->{'cache'}->{$name}->{$type};
}
@@ -662,7 +672,7 @@ sub merge {
foreach my $key (keys %{ $self->{'cache'}->{$name}->{$type} || {} }) {
if (defined $self->{'cache'}->{$name}->{$merged_type}->{$key}) {
- warning("Duplicate key in cache: $name|$merged_type|$key. Skipping.\n");
+ # warning("Duplicate key in cache: $name|$merged_type|$key. Skipping.\n");
} else {
$self->{'cache'}->{$name}->{$merged_type}->{$key} =
$self->{'cache'}->{$name}->{$type}->{$key};
@@ -715,7 +725,11 @@ sub slice_names {
} elsif ($self->conf->param('region')) {
# filter by region (specific slice)
- my $slice = $sa->fetch_by_name($self->conf->param('region'));
+ # don't use SliceAdaptor->fetch_by_name() since this will fail if assembly
+ # versions are different for source and target db
+ my ($cs, $version, $name, $start, $end, $strand) =
+ split(/:/, $self->conf->param('region'));
+ my $slice = $sa->fetch_by_region($cs, $name, $start, $end);
push @slice_names, $slice->name;
} else {
diff --git a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
index 1e3e415167..8eee9a73bb 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
@@ -52,28 +52,28 @@ use Bio::EnsEMBL::IdMapping::ScoredMappingMatrix;
sub score_exons {
my $self = shift;
- $self->logger->log_stamped("Starting exon scoring...\n\n");
+ $self->logger->info("Starting exon scoring...\n\n", 0, 'stamped');
# score using overlaps, then exonerate
my $matrix = $self->overlap_score;
my $exonerate_matrix = $self->exonerate_score($matrix);
# log stats before matrix merging
- $self->logger->log("\nOverlap scoring matrix:\n");
+ $self->logger->info("\nOverlap scoring matrix:\n");
$self->log_matrix_stats($matrix);
- $self->logger->log("\nExonerate scoring matrix:\n");
+ $self->logger->info("\nExonerate scoring matrix:\n");
$self->log_matrix_stats($exonerate_matrix);
# merge matrices
- $self->logger->log_stamped("\nMerging scoring matrices...\n");
+ $self->logger->info("\nMerging scoring matrices...\n", 0, 'stamped');
$matrix->merge($exonerate_matrix);
- $self->logger->log_stamped("Done.\n\n");
+ $self->logger->info("Done.\n\n", 0, 'stamped');
# log stats of combined matrix
- $self->logger->log("Combined scoring matrix:\n");
+ $self->logger->info("Combined scoring matrix:\n");
$self->log_matrix_stats($matrix);
- $self->logger->log_stamped("\nDone with exon scoring.\n\n");
+ $self->logger->info("\nDone with exon scoring.\n\n", 0, 'stamped');
return $matrix;
}
@@ -95,20 +95,20 @@ sub overlap_score {
if (-s $overlap_cache) {
# read from file
- $self->logger->log_stamped("Reading exon overlap scoring matrix from file...\n");
- $self->logger->log("Cache file $overlap_cache.\n", 1);
+ $self->logger->info("Reading exon overlap scoring matrix from file...\n", 0, 'stamped');
+ $self->logger->info("Cache file $overlap_cache.\n", 1);
$matrix->read_from_file;
- $self->logger->log_stamped("Done.\n");
+ $self->logger->info("Done.\n", 0, 'stamped');
} else {
# build scoring matrix
- $self->logger->log("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->log_stamped("Overlap scoring...\n");
+ $self->logger->info("Overlap scoring...\n", 0, 'stamped');
$matrix = $self->build_overlap_scores($matrix);
- $self->logger->log_stamped("Done.\n");
+ $self->logger->info("Done.\n", 0, 'stamped');
}
# write scoring matrix to file
@@ -142,15 +142,15 @@ sub exonerate_score {
if (-s $exonerate_cache) {
# read from file
- $self->logger->log_stamped("Reading exonerate matrix from file...\n");
- $self->logger->log("Cache file $exonerate_cache.\n", 1);
+ $self->logger->info("Reading exonerate matrix from file...\n", 0, 'stamped');
+ $self->logger->info("Cache file $exonerate_cache.\n", 1);
$exonerate_matrix->read_from_file;
- $self->logger->log_stamped("Done.\n");
+ $self->logger->info("Done.\n", 0, 'stamped');
} else {
# build scoring matrix
- $self->logger->log("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);
@@ -164,7 +164,7 @@ sub exonerate_score {
} else {
- $self->logger->log("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");
}
@@ -193,7 +193,7 @@ sub build_overlap_scores {
}
# get sorted list of exon containers
- $self->logger->log_stamped("Reading sorted exons from cache...\n", 1);
+ $self->logger->info("Reading sorted exons from cache...\n", 1, 'stamped');
my @source_exons = $self->sort_exons(
[values %{ $self->cache->get_by_name('exons_by_id', 'source') }]
@@ -202,7 +202,7 @@ sub build_overlap_scores {
[values %{ $self->cache->get_by_name('exons_by_id', 'target') }]
);
- $self->logger->log_stamped("Done.\n", 1);
+ $self->logger->info("Done.\n", 1, 'stamped');
# get first source and target exon container
my $source_ec = shift(@source_exons);
@@ -211,7 +211,7 @@ sub build_overlap_scores {
my %source_overlap = ();
my %target_overlap = ();
- $self->logger->log_stamped("Scoring...\n", 1);
+ $self->logger->info("Scoring...\n", 1, 'stamped');
while ($source_ec or $target_ec) {
@@ -243,7 +243,8 @@ sub build_overlap_scores {
next if (defined($matrix->get_score(
$source_ec->[0]->id, $target_exon->id)));
- $self->overlap_score($source_ec->[0], $target_exon, $matrix);
+ $self->calc_overlap_score($source_ec->[0], $target_exon,
+ $matrix);
}
}
@@ -265,7 +266,7 @@ sub build_overlap_scores {
next if (defined($matrix->get_score(
$source_exon->id, $target_ec->[0]->id)));
- $self->overlap_score($source_exon, $target_ec->[0], $matrix);
+ $self->calc_overlap_score($source_exon, $target_ec->[0], $matrix);
}
}
@@ -274,7 +275,7 @@ sub build_overlap_scores {
}
}
- $self->logger->log_stamped("Done.\n", 1);
+ $self->logger->info("Done.\n", 1, 'stamped');
return $matrix;
}
@@ -312,7 +313,7 @@ sub compare_exon_containers {
# region by exons sizes. 1.0 is full overlap on both exons. Score of at least
# 0,5 are added to the exon scoring matrix.
#
-sub overlap_score {
+sub calc_overlap_score {
my $self = shift;
my $source_exon = shift;
my $target_exon = shift;
@@ -361,8 +362,8 @@ sub run_exonerate {
my $source_file = $self->exon_fasta_file('source');
my $target_file = $self->exon_fasta_file('target');
- my $source_size = -s $source_size;
- my $target_size = -s $target_size;
+ my $source_size = -s $source_file;
+ my $target_size = -s $target_file;
# check if fasta files exist and are not empty
unless ($source_size and $target_size) {
@@ -373,21 +374,21 @@ sub run_exonerate {
my $logpath = ($self->conf->param('logpath')||$self->cache->dump_path).
'/lsf_exonerate';
system("rm -rf $logpath") == 0 or
- $self->logger->log_error("Unable to delete lsf log dir $logpath: $!\n");
+ $self->logger->error("Unable to delete lsf log dir $logpath: $!\n");
system("mkdir -p $logpath") == 0 or
- $self->logger->log_error("Can't create lsf log dir $logpath: $!\n");
+ $self->logger->error("Can't create lsf log dir $logpath: $!\n");
# delete exonerate output from previous runs
my $dumppath = $self->cache->dump_path;
opendir(DUMPDIR, $dumppath) or
- $self->logger->log_error("Can't open $dumppath for reading: $!");
+ $self->logger->error("Can't open $dumppath for reading: $!");
while (defined(my $file = readdir(DUMPDIR))) {
next unless /exonerate_map\.\d+/;
unlink("$dumppath/$file") or
- $self->logger->log_error("Can't delete $dumppath/$file: $!");
+ $self->logger->error("Can't delete $dumppath/$file: $!");
}
closedir(DUMPDIR);
@@ -404,29 +405,37 @@ sub run_exonerate {
#
# run exonerate jobs using lsf
#
- my $exonerate_job = "bsub -J $lsf_name[1-$num_jobs] " .
- " -o $logpath/exonerate.%I.out -e $logpath/exonerate.%I.err" .
- " -q normal -m bc_hosts " .
- " $exonerate_path $source_file $target_file" .
- " --querychunkid \$LSB_JOBINDEX --querychunktotal $num_jobs" .
- " --model affine:local -M 900 --showalignment FALSE --subopt no" .
- " --percent $percent --ryo \"myinfo: \%qi \%ti \%et \%ql \%tl\\n\"" .
- " | grep '^myinfo:' > $dumppath/exonerate_map.\$LSB_JOBINDEX";
-
- $self->logger->log("Submitting $num_jobs exonerate jobs to lsf:\n\n");
- $self->logger->log("$exonerate_job\n\n");
+ local *BSUB;
+ open BSUB, "|bsub -J$lsf_name\[1-$num_jobs\] -o $logpath/exonerate.\%I.out"
+ or $self->logger->error("Could not open open pipe to bsub: $!\n");
+
+ my $exonerate_job = qq{$exonerate_path } .
+ qq{--query $source_file --target $target_file } .
+ q{--querychunkid $LSB_JOBINDEX } .
+ qq{--querychunktotal $num_jobs } .
+ q{--model affine:local -M 900 --showalignment FALSE --subopt no } .
+ qq{--percent $percent } .
+ q{--ryo 'myinfo: %qi %ti %et %ql %tl\n' } .
+ qq{| grep '^myinfo:' > $dumppath/exonerate_map.\$LSB_JOBINDEX} . "\n";
+
+ $self->logger->info("Submitting $num_jobs exonerate jobs to lsf:\n\n");
+ $self->logger->info("$exonerate_job\n\n");
- system("$exonerate_job") == 0
- or $self->logger->log_error("Error submitting exonerate jobs: $!");
+ print BSUB $exonerate_job;
+ $self->logger->error("Error submitting exonerate jobs: $!\n")
+ unless ($? == 0);
+ close BSUB;
# submit depended job to monitor finishing of exonerate jobs
- $self->logger->log_stamped("Waiting for exonerate jobs to finish...\n");
+ $self->logger->info("Waiting for exonerate jobs to finish...\n", 0, 'stamped');
- my $depended_job = "bsub -K -w ended($lsf_name) -q small " .
- " -o $logpath/exonerate_depend.out -e $logpath/exonerate_depend.err" .
- " /bin/true";
+ my $dependent_job = qq{bsub -K -w "ended($lsf_name)" -q small } .
+ qq{-o $logpath/exonerate_depend.out /bin/true};
- $self->logger->log_stamepd("All exonerate jobs finished.\n");
+ system($dependent_job) == 0 or
+ $self->logger->error("Error submitting dependent job: $!\n");
+
+ $self->logger->info("All exonerate jobs finished.\n", 0, 'stamped');
#
# check results
@@ -446,18 +455,18 @@ sub run_exonerate {
}
if (@missing) {
- $self->logger->log("Couldn't find all exonerate output files. These are missing:\n");
+ $self->logger->info("Couldn't find all exonerate output files. These are missing:\n");
foreach (@missing) {
- $self->logger->log("$_\n", 1);
+ $self->logger->info("$_\n", 1);
}
exit(1);
}
if (@error) {
- $self->logger->log("One or more exonerate jobs failed. Check these error files:\n");
+ $self->logger->info("One or more exonerate jobs failed. Check these error files:\n");
foreach (@error) {
- $self->logger->log("$_\n", 1);
+ $self->logger->info("$_\n", 1);
}
exit(1);
@@ -506,7 +515,7 @@ sub write_filtered_exons {
throw('You must provide a ScoredMappingMatrix.');
}
- $self->logger->log_stamped("\nDumping $type exons to fasta file...\n");
+ $self->logger->info("\nDumping $type exons to fasta file...\n", 0, 'stamped');
# don't dump exons shorter than this
my $min_exon_length = $self->conf->param('min_exon_length') || 15;
@@ -552,11 +561,11 @@ sub write_filtered_exons {
# log
my $fmt = "%-30s%10s\n";
- my $size = -e $file;
- $self->logger->log(sprintf($fmt, 'Total exons:', $total_exons), 1);
- $self->logger->log(sprintf($fmt, 'Dumped exons:', $dumped_exons), 1);
- $self->logger->log(sprintf($fmt, 'Dump file size:', parse_bytes($size)), 1);
- $self->logger->log_stamped("Done.\n\n");
+ my $size = -s $file;
+ $self->logger->info(sprintf($fmt, 'Total exons:', $total_exons), 1);
+ $self->logger->info(sprintf($fmt, 'Dumped exons:', $dumped_exons), 1);
+ $self->logger->info(sprintf($fmt, 'Dump file size:', parse_bytes($size)), 1);
+ $self->logger->info("Done.\n\n", 0, 'stamped');
return $dumped_exons;
}
@@ -571,21 +580,20 @@ sub parse_exonerate_results {
throw('You must provide a ScoredMappingMatrix.');
}
- $self->logger->log_stamped("Parsing exonerate results...\n");
+ $self->logger->info("Parsing exonerate results...\n", 0, 'stamped');
# loop over all result files
my $dumppath = $self->cache->dump_path;
my $num_files = 0;
+ my $num_lines = 0;
opendir(DUMPDIR, $dumppath) or
- $self->logger->log_error("Can't open $dumppath for reading: $!");
+ $self->logger->error("Can't open $dumppath for reading: $!");
while (defined(my $file = readdir(DUMPDIR))) {
- next unless /exonerate_map\.\d+/;
+ next unless $file =~ /exonerate_map\.\d+/;
- # counters
$num_files++;
- my $num_lines = 0;
open(F, '<', "$dumppath/$file");
@@ -601,7 +609,7 @@ sub parse_exonerate_results {
my $score = 0;
if ($source_length == 0 or $target_length == 0) {
- $self->logger->log_warning("Alignment length is 0 for $source_id/$target_id.\n");
+ $self->logger->warning("Alignment length is 0 for $source_id/$target_id.\n");
} else {
$score = 2 * $match_length / ($source_length + $target_length);
}
@@ -615,7 +623,7 @@ sub parse_exonerate_results {
closedir(DUMPDIR);
- $self->logger->log_stamped("Done parsing $num_lines lines from $num_files result files.\n");
+ $self->logger->info("Done parsing $num_lines lines from $num_files result files.\n", 0, 'stamped');
return $exonerate_matrix;
}
diff --git a/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
index dec16faba6..f06213822d 100644
--- a/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
@@ -52,7 +52,7 @@ sub score_genes {
throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
}
- $self->logger->log_stamped("Starting gene scoring...\n\n");
+ $self->logger->info("Starting gene scoring...\n\n", 0, 'stamped');
# build scores based on transcript scores
my $matrix = $self->scores_from_transcript_scores($transcript_matrix);
@@ -60,23 +60,23 @@ sub score_genes {
# log stats of combined matrix
my $fmt = "%-40s%10.0f\n";
- $self->logger->log("Scoring matrix:\n");
+ $self->logger->info("Scoring matrix:\n");
- $self->logger->log(sprintf($fmt, "Total source genes:",
- $self->cache->get_count_by_name('genes_by_id', 'source'), 1);
+ $self->logger->info(sprintf($fmt, "Total source genes:",
+ $self->cache->get_count_by_name('genes_by_id', 'source')), 1);
- $self->logger->log(sprintf($fmt, "Scored source genes:",
+ $self->logger->info(sprintf($fmt, "Scored source genes:",
$matrix->get_source_count), 1);
- $self->logger->log(sprintf($fmt, "Total target genes:",
- $self->cache->get_count_by_name('genes_by_id', 'target'), 1);
+ $self->logger->info(sprintf($fmt, "Total target genes:",
+ $self->cache->get_count_by_name('genes_by_id', 'target')), 1);
- $self->logger->log(sprintf($fmt, "Scored target genes:",
+ $self->logger->info(sprintf($fmt, "Scored target genes:",
$matrix->get_target_count), 1);
$self->log_matrix_stats($matrix);
- $self->logger->log("\nDone with transcript scoring.\n\n");
+ $self->logger->info("\nDone with transcript scoring.\n\n");
return $matrix;
}
@@ -101,19 +101,19 @@ sub scores_from_transcript_scores {
if (-s $gene_cache) {
# read from file
- $self->logger->log_stamped("Reading gene scoring matrix from file...\n");
- $self->logger->log("Cache file $gene_cache.\n", 1);
+ $self->logger->info("Reading gene scoring matrix from file...\n", 0, 'stamped');
+ $self->logger->info("Cache file $gene_cache.\n", 1);
$matrix->read_from_file;
- $self->logger->log_stamped("Done.\n");
+ $self->logger->info("Done.\n", 0, 'stamped');
} else {
# build scoring matrix
- $self->logger->log("No gene scoring matrix found. Will build new one.\n");
+ $self->logger->info("No gene scoring matrix found. Will build new one.\n");
- $self->logger->log_stamped("Transcript scoring...\n");
+ $self->logger->info("Gene scoring...\n", 0, 'stamped');
$matrix = $self->build_scores($matrix, $transcript_matrix);
- $self->logger->log_stamped("Done.\n");
+ $self->logger->info("Done.\n", 0, 'stamped');
# write scoring matrix to file
$matrix->write_to_file;
@@ -144,7 +144,7 @@ sub build_scores {
$self->flag_matrix_from_transcript_scores($matrix, $transcript_matrix);
# now calculate the actual scores for the genes in the flag matrix
- $final_matrix = $self->score_matrix_from_flag_matrix($matrix,
+ my $final_matrix = $self->score_matrix_from_flag_matrix($matrix,
$transcript_matrix);
return $final_matrix;
@@ -161,7 +161,7 @@ sub flag_matrix_from_transcript_scores {
my $num_genes =
scalar(keys %{ $self->cache->get_by_name('genes_by_id', 'source') });
- $self->logger->log("Creating flag matrix...\n", 1);
+ $self->logger->info("Creating flag matrix...\n", 1);
# for every transcript scoring matrix entry, make an entry in the gene flag
# matrix.
@@ -178,7 +178,7 @@ sub flag_matrix_from_transcript_scores {
$matrix->add_score($source_gene->id, $target_gene->id, 1);
}
- $self->logger->log("\n\n");
+ $self->logger->info("\n\n");
return $matrix;
}
@@ -201,7 +201,7 @@ sub score_matrix_from_flag_matrix {
my $num_genes =
scalar(keys %{ $self->cache->get_by_name('genes_by_id', 'source') });
- $self->logger->log("Creating score matrix from flag matrix...\n", 1);
+ $self->logger->info("Creating score matrix from flag matrix...\n", 1);
# loop over flag matrix and do proper scoring for each entry
foreach my $entry (@{ $flag_matrix->get_all_Entries }) {
@@ -230,7 +230,7 @@ sub score_matrix_from_flag_matrix {
$matrix->add($entry->source, $entry->target, $score);
}
- $self->logger->log("\n\n");
+ $self->logger->info("\n\n");
return $matrix;
}
@@ -254,7 +254,7 @@ sub complex_gene_gene_score {
@{ $target_gene->get_all_Transcripts };
# loop over source transcripts
- foreach my $source_transcript (@{ $source_gene->get_all_Transcripts ) {
+ foreach my $source_transcript (@{ $source_gene->get_all_Transcripts }) {
# now loop over target transcripts and find the highest scoring target
# transcript belonging to the target gene
@@ -262,7 +262,7 @@ sub complex_gene_gene_score {
foreach my $target_transcript_id (@{ $transcript_matrix->get_targets_for_source($source_transcript->id) }) {
- next unless (%target_transcripts{$target_transcript_id});
+ next unless ($target_transcripts{$target_transcript_id});
my $score = $transcript_matrix->get_score(
$source_transcript->id, $target_transcript_id);
@@ -281,7 +281,7 @@ sub complex_gene_gene_score {
@{ $source_gene->get_all_Transcripts };
# loop over target transcripts
- foreach my $target_transcript (@{ $target_gene->get_all_Transcripts ) {
+ foreach my $target_transcript (@{ $target_gene->get_all_Transcripts }) {
# now loop over source transcripts and find the highest scoring source
# transcript belonging to the source gene
@@ -289,7 +289,7 @@ sub complex_gene_gene_score {
foreach my $source_transcript_id (@{ $transcript_matrix->get_sources_for_target($target_transcript->id) }) {
- next unless (%source_transcripts{$source_transcript_id});
+ next unless ($source_transcripts{$source_transcript_id});
my $score = $transcript_matrix->get_score(
$source_transcript_id, $target_transcript->id);
@@ -306,14 +306,14 @@ sub complex_gene_gene_score {
# calculate overall score for this gene
my $gene_score = 0;
- if (($source_gene_length + $target_gene_length) > 0) {
+ if (($source_gene->length + $target_gene->length) > 0) {
$gene_score = ($source_gene_score + $target_gene_score) /
- ($source_gene_length + $target_gene_length);
+ ($source_gene->length + $target_gene->length);
} else {
- $self->logger->log_warning("Combined length of source (".$source_gene->id.") and target (".$target_gene->id.") gene is zero!\n", 1);
+ $self->logger->warning("Combined length of source (".$source_gene->id.") and target (".$target_gene->id.") gene is zero!\n", 1);
}
@@ -326,7 +326,7 @@ sub complex_gene_gene_score {
# This is used when the more elaborate gene representing score does not
# distinguish very well.
#
-sub complex_gene_gene_score {
+sub simple_gene_gene_score {
my $self = shift;
my $source_gene = shift;
my $target_gene = shift;
@@ -334,8 +334,8 @@ sub complex_gene_gene_score {
my $gene_score = 0;
- foreach my $source_transcript (@{ $source_gene->get_all_Transcripts ) {
- foreach my $target_transcript (@{ $target_gene->get_all_Transcripts ) {
+ foreach my $source_transcript (@{ $source_gene->get_all_Transcripts }) {
+ foreach my $target_transcript (@{ $target_gene->get_all_Transcripts }) {
my $score = $transcript_matrix->get_score($source_transcript->id,
$target_transcript->id);
diff --git a/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
index 15aaf86661..4f6403e68e 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
@@ -111,15 +111,15 @@ sub log_matrix_stats {
my $fmt1 = "%-40s%10.0f\n";
my $fmt2 = "%-40s%10.2f\n";
- $self->logger->log(sprintf($fmt1, "Scoring matrix entries:",
+ $self->logger->info(sprintf($fmt1, "Scoring matrix entries:",
$matrix->get_entry_count), 1);
- $self->logger->log(sprintf($fmt2, "Average score:",
+ $self->logger->info(sprintf($fmt2, "Average score:",
$matrix->get_average_score), 1);
my ($min, $max) = @{ $matrix->get_min_max_scores };
- $self->logger->log(sprintf($fmt2, "Min. score:", $min), 1);
- $self->logger->log(sprintf($fmt2, "Max. score:", $max), 1);
+ $self->logger->info(sprintf($fmt2, "Min. score:", $min), 1);
+ $self->logger->info(sprintf($fmt2, "Max. score:", $max), 1);
}
diff --git a/modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm b/modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm
index e06371e7aa..4ff78b6ad3 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm
@@ -156,27 +156,32 @@ sub get_all_Entries {
sub get_all_sources {
- return [keys %{ $_->{'source_list'} }];
+ my $self = shift;
+ return [keys %{ $self->{'cache'}->{'source_list'} }];
}
sub get_all_targets {
- return [keys %{ $_->{'target_list'} }];
+ my $self = shift;
+ return [keys %{ $self->{'cache'}->{'target_list'} }];
}
sub get_entry_count {
- return scalar(keys %{ $_->{'matrix'} });
+ my $self = shift;
+ return scalar(keys %{ $self->{'cache'}->{'matrix'} });
}
sub get_source_count {
- return scalar(keys %{ $_->{'source_list'} });
+ my $self = shift;
+ return scalar(keys %{ $self->{'cache'}->{'source_list'} });
}
sub get_target_count {
- return scalar(keys %{ $_->{'target_list'} });
+ my $self = shift;
+ return scalar(keys %{ $self->{'cache'}->{'target_list'} });
}
@@ -228,10 +233,10 @@ sub merge {
my $c = 0;
- foreach my $key (keys %{ $matrix->{'matrix'} }) {
+ foreach my $key (keys %{ $matrix->{'cache'}->{'matrix'} }) {
if (!defined($self->{'cache'}->{'matrix'}->{$key}) or
- $self->{'cache'}->{'matrix'}->{$key} < $matrix->{'matrix'}->{$key}) {
- $self->{'cache'}->{'matrix'}->{$key} = $matrix->{'matrix'}->{$key};
+ $self->{'cache'}->{'matrix'}->{$key} < $matrix->{'cache'}->{'matrix'}->{$key}) {
+ $self->{'cache'}->{'matrix'}->{$key} = $matrix->{'cache'}->{'matrix'}->{$key};
$c++;
}
}
diff --git a/modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm
index 815a8c64b1..354c07a988 100644
--- a/modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm
@@ -52,7 +52,7 @@ sub score_transcripts {
throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
}
- $self->logger->log_stamped("Starting transcript scoring...\n\n");
+ $self->logger->info("Starting transcript scoring...\n\n", 0, 'stamped');
# build scores based on exon scores
my $matrix = $self->scores_from_exon_scores($exon_matrix);
@@ -60,23 +60,23 @@ sub score_transcripts {
# log stats of combined matrix
my $fmt = "%-40s%10.0f\n";
- $self->logger->log("Scoring matrix:\n");
+ $self->logger->info("Scoring matrix:\n");
- $self->logger->log(sprintf($fmt, "Total source transcripts:",
- $self->cache->get_count_by_name('transcripts_by_id', 'source'), 1);
+ $self->logger->info(sprintf($fmt, "Total source transcripts:",
+ $self->cache->get_count_by_name('transcripts_by_id', 'source')), 1);
- $self->logger->log(sprintf($fmt, "Scored source transcripts:",
+ $self->logger->info(sprintf($fmt, "Scored source transcripts:",
$matrix->get_source_count), 1);
- $self->logger->log(sprintf($fmt, "Total target transcripts:",
- $self->cache->get_count_by_name('transcripts_by_id', 'target'), 1);
+ $self->logger->info(sprintf($fmt, "Total target transcripts:",
+ $self->cache->get_count_by_name('transcripts_by_id', 'target')), 1);
- $self->logger->log(sprintf($fmt, "Scored target transcripts:",
+ $self->logger->info(sprintf($fmt, "Scored target transcripts:",
$matrix->get_target_count), 1);
$self->log_matrix_stats($matrix);
- $self->logger->log("\nDone with transcript scoring.\n\n");
+ $self->logger->info("\nDone with transcript scoring.\n\n");
return $matrix;
}
@@ -101,19 +101,19 @@ sub scores_from_exon_scores {
if (-s $transcript_cache) {
# read from file
- $self->logger->log_stamped("Reading transcript scoring matrix from file...\n");
- $self->logger->log("Cache file $transcript_cache.\n", 1);
+ $self->logger->info("Reading transcript scoring matrix from file...\n", 0, 'stamped');
+ $self->logger->info("Cache file $transcript_cache.\n", 1);
$matrix->read_from_file;
- $self->logger->log_stamped("Done.\n");
+ $self->logger->info("Done.\n", 0, 'stamped');
} else {
# build scoring matrix
- $self->logger->log("No transcript scoring matrix found. Will build new one.\n");
+ $self->logger->info("No transcript scoring matrix found. Will build new one.\n");
- $self->logger->log_stamped("Transcript scoring...\n");
+ $self->logger->info("Transcript scoring...\n", 0, 'stamped');
$matrix = $self->build_scores($matrix, $exon_matrix);
- $self->logger->log_stamped("Done.\n");
+ $self->logger->info("Done.\n", 0, 'stamped');
# write scoring matrix to file
$matrix->write_to_file;
@@ -144,7 +144,8 @@ sub build_scores {
$self->flag_matrix_from_exon_scores($matrix, $exon_matrix);
# now calculate the actual scores for the transcripts in the flag matrix
- $final_matrix = $self->score_matrix_from_flag_matrix($matrix, $exon_matrix);
+ my $final_matrix =
+ $self->score_matrix_from_flag_matrix($matrix, $exon_matrix);
return $final_matrix;
}
@@ -160,7 +161,7 @@ sub flag_matrix_from_exon_scores {
my $num_transcripts =
scalar(keys %{ $self->cache->get_by_name('transcripts_by_id', 'source') });
- $self->logger->log("Creating flag matrix...\n", 1);
+ $self->logger->info("Creating flag matrix...\n", 1);
# loop over source transcripts
foreach my $source_transcript (values %{ $self->cache->get_by_name('transcripts_by_id', 'source') }) {
@@ -169,7 +170,7 @@ sub flag_matrix_from_exon_scores {
$self->logger->log_progress($num_transcripts, ++$i, 20, 1, 0);
# get all exons for the source transcript
- foreach my $source_exon (@{ $souce_transcript->get_all_Exons }) {
+ foreach my $source_exon (@{ $source_transcript->get_all_Exons }) {
# get target exons for this source exon from scoring matrix
foreach my $target_exon_id (@{ $exon_matrix->get_targets_for_source($source_exon->id) }) {
@@ -178,14 +179,14 @@ sub flag_matrix_from_exon_scores {
foreach my $target_transcript (@{ $self->cache->get_by_key('transcripts_by_exon_id', 'target', $target_exon_id) }) {
# add scoring flag for these two transcripts
- $matrix->add_score($source_transcript->id, $target_transcript->id, 1)Ã;
+ $matrix->add_score($source_transcript->id, $target_transcript->id, 1);
}
}
}
}
- $self->logger->log("\n\n");
+ $self->logger->info("\n\n");
return $matrix;
}
@@ -210,7 +211,7 @@ sub score_matrix_from_flag_matrix {
my $num_transcripts =
scalar(keys %{ $self->cache->get_by_name('transcripts_by_id', 'source') });
- $self->logger->log("Creating score matrix from flag matrix...\n", 1);
+ $self->logger->info("Creating score matrix from flag matrix...\n", 1);
# loop over source transcripts
foreach my $source_transcript (values %{ $self->cache->get_by_name('transcripts_by_id', 'source') }) {
@@ -247,7 +248,7 @@ sub score_matrix_from_flag_matrix {
foreach my $target_exon_id (@{ $exon_matrix->get_targets_for_source($source_exon->id) }) {
- next unless (%target_exon{$target_exon_id});
+ next unless ($target_exons{$target_exon_id});
my $score = $exon_matrix->get_score(
$source_exon->id, $target_exon_id);
@@ -266,7 +267,7 @@ sub score_matrix_from_flag_matrix {
foreach my $source_exon_id (@{ $exon_matrix->get_sources_for_target($target_exon->id) }) {
- next unless (%source_exon{$source_exon_id});
+ next unless ($source_exons{$source_exon_id});
my $score = $exon_matrix->get_score(
$source_exon_id, $target_exon->id);
@@ -287,7 +288,7 @@ sub score_matrix_from_flag_matrix {
if (($source_transcript_score > $source_transcript_length) or
($target_transcript_score > $target_transcript_length)) {
- $self->logger->log_warning("Score > length for source ($source_target_score <> $source_transcript_length) or target ($target_transcript_score <> $target_transcript_length).\n", 1);
+ $self->logger->warning("Score > length for source ($source_transcript_score <> $source_transcript_length) or target ($target_transcript_score <> $target_transcript_length).\n", 1);
} else {
@@ -305,14 +306,14 @@ sub score_matrix_from_flag_matrix {
} else {
- $self->logger->log_warning("Combined length of source (".$source_transcript->id.") and target (".$target_transcript->id.") transcript is zero!\n", 1);
+ $self->logger->warning("Combined length of source (".$source_transcript->id.") and target (".$target_transcript->id.") transcript is zero!\n", 1);
}
}
}
- $self->logger->log("\n\n");
+ $self->logger->info("\n\n");
return $matrix;
--
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