diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 50a044169f2a4a19e7476b4e9d9feebb0f0b861a..4a9fac64b2c157294fa020f8e9cd7abb0bdb11a0 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -32,6 +32,10 @@ Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
=cut
+# Hashes to hold method-specific thresholds
+my %method_query_threshold;
+my %method_target_threshold;
+
=head2 dump_seqs
Arg[1]: xref object which holds info needed for the dump of xref
@@ -87,11 +91,7 @@ sub build_list_and_map {
$i++;
}
- if (!defined($self->use_existing_mappings)) {
- $self->run_mapping(\@list);
- } else {
- print "Using existing mappings";
- }
+ $self->run_mapping(\@list);
}
@@ -583,11 +583,17 @@ sub run_mapping {
my ($self, $lists) = @_;
- # delete old output files in target directory
- my $dir = $self->dir();
- unlink (<$dir/*.map $dir/*.out $dir/*.err>);
+ # delete old output files in target directory if we're going to produce new ones
+ if (!defined($self->use_existing_mappings)) {
+ my $dir = $self->dir();
+ unlink (<$dir/*.map $dir/*.out $dir/*.err>);
+ }
# foreach method, submit the appropriate job & keep track of the job name
+ # note we check if use_existing_mappings is set here, not earlier, as we
+ # still need to instantiate the method object in order to fill
+ # method_query_threshold and method_target_threshold
+
my @job_names;
foreach my $list (@$lists){
@@ -604,17 +610,22 @@ sub run_mapping {
} else {
my $obj = $obj_name->new();
- my $job_name = $obj->run($queryfile, $targetfile, $self->dir());
- push @job_names, $job_name;
- sleep 1; # make sure unique names really are unique
+ $method_query_threshold{$method} = $obj->query_identity_threshold();
+ $method_target_threshold{$method} = $obj->target_identity_threshold();
+ if (!defined($self->use_existing_mappings)) {
+ my $job_name = $obj->run($queryfile, $targetfile, $self->dir());
+ push @job_names, $job_name;
+ sleep 1; # make sure unique names really are unique
+ }
}
} # foreach method
- # submit depend job to wait for all mapping jobs
- submit_depend_job($self->dir, @job_names);
-
+ if (!defined($self->use_existing_mappings)) {
+ # submit depend job to wait for all mapping jobs
+ submit_depend_job($self->dir, @job_names);
+ }
} # run_mapping
@@ -669,7 +680,7 @@ sub submit_depend_job {
}
-=head2 store
+=head2 generate_core_xrefs
Arg[1] : The target file used in the exonerate run. Used to work out the Ensembl object type.
Arg[2] :
@@ -681,7 +692,7 @@ sub submit_depend_job {
=cut
-sub store {
+sub generate_core_xrefs {
my ($self, $xref) = @_;
@@ -745,6 +756,8 @@ sub store {
# files are named Method_(dna|peptide)_N.map
my $type = get_ensembl_object_type($file);
+ my $method = get_method($file);
+
# get or create the appropriate analysis ID
# XXX restore when using writeable database
#my $analysis_id = $self->get_analysis_id($type);
@@ -763,8 +776,9 @@ sub store {
# TODO make sure query & target are the right way around
- # only take mappings where there is a good match on or both sequences
- #next if ($query_identity < 98 and $target_identity < 98);
+ # only take mappings where there is a good match on one or both sequences
+ next if ($query_identity < $method_query_threshold{$method} &&
+ $target_identity < $method_target_threshold{$method});
# note we add on $xref_id_offset to avoid clashes
print OBJECT_XREF "$object_xref_id\t$target_id\t$type\t" . ($query_id+$xref_id_offset) . "\n";
@@ -838,6 +852,17 @@ sub get_ensembl_object_type {
}
+sub get_method {
+
+ my $filename = shift;
+
+ $filename = basename($filename);
+
+ my ($method) = $filename =~ /^(.*)_(dna|peptide)_\d+\.map/;
+
+ return $method;
+
+}
sub get_analysis_id {
@@ -947,7 +972,7 @@ sub dump_core_xrefs {
# write to file and add to object_xref_mappings
if (defined $xref_to_objects{$master_xref_id}) { # XXX check
my @ensembl_object_ids = keys( %{$xref_to_objects{$master_xref_id}} ); # XXX check
- print "xref $accession has " . scalar(@ensembl_object_ids) . " associated ensembl objects\n";
+ #print "xref $accession has " . scalar(@ensembl_object_ids) . " associated ensembl objects\n";
foreach my $object_id (@ensembl_object_ids) {
my $type = $ensembl_object_types{$object_id};
print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "\tDEPENDENT\n";
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
index f7b68f4f88814b124f8cb9c6a4b9d5fdc6ec7323..b5a02b8e89bf56a09249643d02ff0041fc99fd5b 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
@@ -174,11 +174,11 @@ sub get_class_name() {
my $self = shift;
- $self =~ s/=.*$//;
+ my $module_name = ref($self);
- my @bits = split(/::/, $self);
+ my @bits = split(/::/, $module_name);
- return @bits[$#bits];
+ return $bits[-1];
}
@@ -196,5 +196,22 @@ sub check_err {
}
}
+# Percentage identity that query (xref) must match to be considered.
+
+sub query_identity_threshold {
+
+ return 98;
+
+}
+
+
+# Percentage identity that target (ensembl) must match to be considered.
+
+sub target_identity_threshold {
+
+ return 98;
+
+}
+
1;
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateUngappedBest1.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateUngappedBest1.pm
index 833535b1ed54db7453e942a7a022d02e06f91715..80ab7ec1deae3c4fb3212dcc6870ed1315ee8b80 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateUngappedBest1.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateUngappedBest1.pm
@@ -15,5 +15,16 @@ sub options {
}
+sub query_identity_threshold {
+
+ return 100;
+
+}
+
+sub target_identity_threshold {
+
+ return 100;
+
+}
1;