From 6eb5165c3bbf7f9c2b69f797c46fd05fb2fe63f5 Mon Sep 17 00:00:00 2001
From: jason <jason@bioperl.org>
Date: Thu, 21 Jun 2001 21:02:59 +0000
Subject: [PATCH] added -online flag, -debug flag handle duplicated markers by
 merging information into existing marker

svn path=/bioperl-db/trunk/; revision=265
---
 Bio/DB/Map/SQL/MarkerAdaptor.pm   | 11 +++++++----
 scripts/load_genethon_data.pl     | 17 ++++++-----------
 scripts/load_marshfield_map.pl    | 15 ++++++---------
 scripts/load_whitehead_markers.pl | 19 ++++++++-----------
 4 files changed, 27 insertions(+), 35 deletions(-)

diff --git a/Bio/DB/Map/SQL/MarkerAdaptor.pm b/Bio/DB/Map/SQL/MarkerAdaptor.pm
index 9bc7bf5..2b6b26b 100644
--- a/Bio/DB/Map/SQL/MarkerAdaptor.pm
+++ b/Bio/DB/Map/SQL/MarkerAdaptor.pm
@@ -224,7 +224,6 @@ sub write {
 	foreach my $alias ( $marker->each_alias ) {
 	    my $src = $marker->get_source_for_alias($alias);
 	    eval { 
-
 		if( ! $markercopy->is_alias($alias) ) {
 		    $sth->execute($alias,$marker->id, $src);
 		} elsif( $markercopy->get_source_for_alias($alias) ne 
@@ -232,9 +231,13 @@ sub write {
 		    $sthupdate->execute($src, $marker->id, $alias);
 		}
 	    };
-	    if( $@) {
-		$self->warn($@);
-		$rc = -1 unless ( $@ =~ /Duplicate/ );
+	    if( $@) {		
+		if ( $@ =~ /Duplicate entry/ ) {
+		    $self->warn($@) if( $self->verbose >= 1);
+		} else {
+		    $rc = -1;
+		    $self->warn($@);
+		}
 	    }
 	}
 	$sth->finish();
diff --git a/scripts/load_genethon_data.pl b/scripts/load_genethon_data.pl
index 3a3a408..e123ca0 100755
--- a/scripts/load_genethon_data.pl
+++ b/scripts/load_genethon_data.pl
@@ -33,6 +33,8 @@ my $dbpass = 'undef';
 my $module = 'Bio::DB::Map::SQL::DBAdaptor';
 
 &GetOptions( 
+	     'online'          => \$ONLINE,
+	     'debug'           => \$DEBUG,
 	     'host:s'          => \$host,
 	     'port:n'          => \$port,
 	     'db|dbname:s'     => \$dbname,
@@ -61,7 +63,7 @@ foreach my $chrom ( 1..23 ) {
     my ($DATA) = &get_genethon_data($chrom);
     
     while(<$DATA>) {
-	
+	s/\*//g;
 	my ($probe,$sexavg,$female,$male,$locus,$genbank,
 	    $allelect,$heterozygosity,$fwd,$rev,$genotype,$minmax);
 	if( $chrom < 23 ) {
@@ -105,18 +107,11 @@ foreach my $marker ( values %markers ) {
 	$count++;
     }
     if( ! $markeradaptor->write($marker) ) {
-	my ( $markercopy ) = $markeradaptor->get('-pcrprimers' => [ $marker->pcrfwd,
-							     $marker->pcrrev ] );
 	$duplicate++;
-	if( $markercopy ) {
-	    $marker->id($markercopy->id);
-	    $markeradaptor->write($marker);
-	} else { 
-	    print "unable to find marker for primers ", $marker->pcrfwd, 
-	    ", ", $marker->pcrrev, "\n";
-	}
-    }
+	$markeradaptor->add_duplicate_marker($marker);	
+    }    
 }
+
 print "No primers for $count, $duplicate duplicates, out of $total\n";
 
 sub get_genethon_data {
diff --git a/scripts/load_marshfield_map.pl b/scripts/load_marshfield_map.pl
index c1fbcb6..a938b8b 100755
--- a/scripts/load_marshfield_map.pl
+++ b/scripts/load_marshfield_map.pl
@@ -36,6 +36,8 @@ my $dbpass = 'undef';
 my $module = 'Bio::DB::Map::SQL::DBAdaptor';
 
 &GetOptions( 
+	     'online'          => \$ONLINE,
+	     'debug'           => \$DEBUG,
 	     'host:s'          => \$host,
 	     'port:n'          => \$port,
 	     'db|dbname:s'     => \$dbname,
@@ -184,17 +186,12 @@ foreach my $marker ( values %markers ) {
 				 $marker->to_string);
 	}
 	$count++;
-    }
+	next;
+    }    
     if( ! $markeradaptor->write($marker) ) {
-	my ( $markercopy ) = $markeradaptor->get('-pcrprimers' => [ $marker->pcrfwd,
-							     $marker->pcrrev ] );
 	$duplicate++;
-	if( $markercopy ) {
-	    $marker->id($markercopy->id);
-	    $markeradaptor->write($marker);
-	} else { 
-	    print "unable to find marker for primers ", $marker->pcrfwd, 
-	    ", ", $marker->pcrrev, "\n";
+	if( ! $markeradaptor->add_duplicate_marker($marker) ) {
+	    print STDERR "no duplicate marker found for ", $marker->to_string(), "\n";
 	}
     }
 }
diff --git a/scripts/load_whitehead_markers.pl b/scripts/load_whitehead_markers.pl
index 73cbd0f..9c25422 100755
--- a/scripts/load_whitehead_markers.pl
+++ b/scripts/load_whitehead_markers.pl
@@ -41,6 +41,8 @@ my $dbpass = 'undef';
 my $module = 'Bio::DB::Map::SQL::DBAdaptor';
 
 &GetOptions( 
+	     'online'          => \$ONLINE,
+	     'debug'           => \$DEBUG,
 	     'host:s'          => \$host,
 	     'port:n'          => \$port,
 	     'db|dbname:s'     => \$dbname,
@@ -81,7 +83,6 @@ while(<$STS>) {
 	
 	next;
     }
-
     my $marker = new Bio::DB::Map::Marker ( -probe => $assay,
 					    -locus => $locus,
 					    -chrom => $chrom,
@@ -189,24 +190,20 @@ foreach my $marker ( values %markers ) {
 	$count++;
 	next;	    
     } 
-    
+
     if( ! $markeradaptor->write($$marker) ) {
 	$duplicate++;
-	my ( $markercopy ) = $markeradaptor->get('-pcrprimers' => [ $$marker->pcrfwd,
-							     $$marker->pcrrev ] );
-	if( $markercopy ) {
-	    $$marker->id($markercopy->id);
-	    $markeradaptor->write($$marker);
-	}
-    }
+	$markeradaptor->add_duplicate_marker($$marker);	
+    }    
 }
 print "skipped $count, $duplicate duplicates out of $total\n";
 
 sub get_data_for_chrom {
     my ($chrom) = @_;
+    $chrom =~ s/23/X/;
     my $fh;
     if( $ONLINE ) {
-	my $url = sprintf('%s/Chr%d.rh', $WHITEHEADRHMAP,$chrom);
+	my $url = sprintf('%s/Chr%s.rh', $WHITEHEADRHMAP,$chrom);
 	my $request = GET $url;
 	my $response = $ua->request($request);
 	if( $response->is_success ) {
@@ -218,7 +215,7 @@ sub get_data_for_chrom {
 	    $fh = undef;
 	}
     } else {
-	my $file = sprintf('< %s/Chr%d.rh', $WHITEHEADRHMAPDIR,
+	my $file = sprintf('< %s/Chr%s.rh', $WHITEHEADRHMAPDIR,
 			   $chrom);
 	$fh = new IO::File($file) or do { 
 	    warn("cannot open $file");
-- 
2.11.4.GIT