From a449408df3420b667990fb081b47fcdb06628e4f Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 16 Mar 2009 15:25:59 +0000
Subject: [PATCH] help and a bug fix
---
misc-scripts/xref_mapping/xref_mapper.pl | 78 ++++++++++++++++++------
1 file changed, 58 insertions(+), 20 deletions(-)
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index 674186d2d0..c032bfa416 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -35,18 +35,11 @@ GetOptions ('file=s' => \$file,
'dumpcheck' => \$dumpcheck,
'upload' => \$upload,
'verbose' => \$verbose,
- 'nofarm' => \$nofarm );
+ 'nofarm' => \$nofarm,
+ 'help' => sub { usage(); exit(0); } );
-
-my $mapper = XrefMapper::SubmitMapper->process_file($file);
-
-########################TEST########################
-#my $core_info = XrefMapper::CoreInfo->new($mapper);
-#$core_info->test_return_codes();
-#exit;
-####################################################
-
+my $mapper = XrefMapper::BasicMapper->process_file($file, $verbose);
if(defined($dumpcheck)){
@@ -67,21 +60,21 @@ my $status = $mapper->xref_latest_status($mapper->verbose);
print "current status is $status\n" if ($mapper->verbose);
+my $submitter = XrefMapper::SubmitMapper->new($mapper);
if( $status eq "parsing_finished"){
print "\nDumping xref & Ensembl sequences\n" if ($mapper->verbose);
- $mapper->dump_seqs();
- $status = $mapper->xref_latest_status();
+ $submitter->dump_seqs();
}
else{
- $mapper->no_dump_xref()
+ $submitter->no_dump_xref()
}
$status = $mapper->xref_latest_status();
if($status eq "core_fasta_dumped"){
- $mapper->build_list_and_map();
+ $submitter->build_list_and_map();
$status = $mapper->xref_latest_status();
}
else{
@@ -120,7 +113,6 @@ if($status eq "prioritys_flagged"){ # process the inferred pairs and interpro x
my $inter = XrefMapper::Interpro->new($mapper);
$inter->process();
}
-#$mapper->biomart_test();
# Biomart test each external_db on one ensembl type only and fix it
@@ -132,13 +124,10 @@ if($status eq "processed_pairs"){
# species specific processing
# i.e. for mouse and human add MGI_curated_gene and HGNC_curated_gene
-#$mapper->biomart_test();
-
$status = $mapper->xref_latest_status();
if($status eq "processed_pairs"){
$mapper->official_naming();
}
-#$mapper->biomart_test();
# Coordinate xrefs
@@ -161,11 +150,14 @@ if($status eq "tests_finished" and $upload){
my $coord = XrefMapper::CoordinateMapper->new($mapper);
$coord->run_coordinatemapping($upload);
-
+}
+
+$status = $mapper->xref_latest_status();
+if($status eq "coordinate_xref_finished" and $upload){
my $loader = XrefMapper::XrefLoader->new($mapper);
$loader->update();
-
+
}
# generate display_xrefs and descriptions for gene and transcripts.
@@ -178,6 +170,52 @@ if(($status eq "core_loaded" or $status eq "display_xref_done") and $upload){
}
+sub usage {
+
+ print << "EOF";
+ xref_mapper.pl -file {config_file} -verbose -upload -nofarm
+
+ -file Name of configuration file.
+ For more info on this file see end of help.
+
+ -dumpcheck Check if the fasta files already exist.
+ If so do not redump them.
+
+ -upload Write data from xref database to core database.
+
+ -verbose Give information about progress and possible warnings.
+ (Very much recomended)
+
+ -nofarm Run the exonerate jobs locally and not on the compute farm.
+
+
+Below is an example of the configuration file
+####################################################
+xref
+host=host1
+port=3306
+dbname=hedgehog_xref_54
+user=user1
+password=pass1
+dir=./xref
+
+species=erinaceus_europaeus
+host=host2
+port=3306
+dbname=erinaceus_europaeus_core_54_1e
+user=user2
+password=pass2
+dir=./ensembl
+####################################################
+host1 can be the same as host2.
+user1 can be the same as user2 but user2 must have write access and user1 must have at least read access.
+The directorys set by dir= must already exist.
+
+
+
+EOF
+
+}
--
GitLab