From bd8a7bc668e5ed560636cfa045ef1f7055372d9b Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Tue, 12 Oct 2004 09:24:14 +0000
Subject: [PATCH] store() now looks in correct directory for exonerate output
files.
Documentation.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 54 +++++++++++++------
1 file changed, 39 insertions(+), 15 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 2a68fe1ae0..20fa16e5c0 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -2,6 +2,7 @@ package XrefMapper::BasicMapper;
use strict;
use DBI;
+use IPC::Open3;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Translation;
use XrefMapper::db;
@@ -83,7 +84,7 @@ sub run_matching{
push @list, \@pep;
$i++;
}
-
+
$self->run_mapping(\@list);
}
@@ -141,11 +142,14 @@ sub get_species_id_from_species_name{
=cut
sub get_set_lists{
- my ($self) = @_;
+ my ($self) = @_;
+
+# return [["method1",["homo_sapiens","RefSeq"],["homo_sapiens","UniProtSwissProt"]],
+# ["method2",[$self->species,"*"]],
+# ["method3",["*","*"]]];
+
+ return [["ExonerateBest1",["homo_sapiens","RefSeq"]]];
- return [["method1",["homo_sapiens","RefSeq"],["homo_sapiens","UniProtSwissProt"]],
- ["method2",[$self->species,"*"]],
- ["method3",["*","*"]]];
}
=head2 get_source_id_from_source_name
@@ -535,11 +539,18 @@ sub method{
return $self->{_method};
}
-# --------------------------------------------------------------------------------
-# GLENN
+=head2 run_mapping
-# Use exonerate (or other program) to find xref-ensembl obejct mappings
+ Arg[1] : List of lists of (method, query, target)
+ Arg[2] :
+ Example : none
+ Description: Create and submit mapping jobs to LSF, and wait for them to finish.
+ Returntype : none
+ Exceptions : none
+ Caller : general
+
+=cut
sub run_mapping {
@@ -552,7 +563,7 @@ sub run_mapping {
my ($method, $queryfile ,$targetfile) = @$list;
- print "###$method $queryfile $targetfile\n";
+ print "Method:$method Query:$queryfile Target:$targetfile\n";
my $obj_name = "XrefMapper::Methods::$method";
# check that the appropriate object exists
@@ -564,9 +575,9 @@ sub run_mapping {
} else {
my $obj = $obj_name->new();
- my $job_name = $obj->run($queryfile, $targetfile);
+ my $job_name = $obj->run($queryfile, $targetfile, $self->dir());
push @job_names, $job_name;
- print "Submitted LSF job $job_name to list\n";
+ print "Added LSF job $job_name to list\n";
sleep 1; # make sure unique names really are unique
}
@@ -580,6 +591,18 @@ sub run_mapping {
} # run_exonerate
+=head2 submit_depend_job
+
+ Arg[1] : List of job names.
+ Arg[2] :
+ Example : none
+ Description: Submit an LSF job that waits for other jobs to finish.
+ Returntype : none
+ Exceptions : none
+ Caller : general
+
+=cut
+
sub submit_depend_job {
my ($root_dir, @job_names) = @_;
@@ -621,7 +644,7 @@ sub submit_depend_job {
=head2 store
Arg[1] : The target file used in the exonerate run. Used to work out the Ensembl object type.
- Arg[2] :
+ Arg[2] :
Example : none
Description: Parse exonerate output files and build files for loading into target db tables.
Returntype : List of strings
@@ -632,7 +655,7 @@ sub submit_depend_job {
sub store {
- my ($target_file_name) = @_;
+ my ($self, $target_file_name) = @_;
my $type = get_ensembl_object_type($target_file_name);
@@ -645,7 +668,7 @@ sub store {
"ensembl",
{'RaiseError' => 1}) || die "Can't connect to database";
- # get current max object_xref_id
+ # get current max object_xref_id
my $max_object_xref_id = 0;
my $sth = $dbi->prepare("SELECT MAX(object_xref_id) FROM object_xref");
$sth->execute();
@@ -673,7 +696,8 @@ sub store {
# keep a (unique) list of xref IDs that need to be written out to file as well
my %primary_xref_ids;
- foreach my $file (glob("*.map")) {
+ my $dir = $self->dir();
+ foreach my $file (glob("$dir/*.map")) {
print "Parsing results from $file \n";
open(FILE, $file);
--
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