From 4e203e91af9304b3af34196ef361e677680f8d01 Mon Sep 17 00:00:00 2001
From: Philip Lijnzaad <lijnzaad@sanger.ac.uk>
Date: Wed, 10 Oct 2001 15:09:19 +0000
Subject: [PATCH] dumping of contig_landMarkMarkers was missing. also using
strict now.
---
misc-scripts/utilities/make_dbdump_bychr.pl | 22 +++++++++++++++++----
1 file changed, 18 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/utilities/make_dbdump_bychr.pl b/misc-scripts/utilities/make_dbdump_bychr.pl
index 26a61a8f80..117431e1ca 100644
--- a/misc-scripts/utilities/make_dbdump_bychr.pl
+++ b/misc-scripts/utilities/make_dbdump_bychr.pl
@@ -24,6 +24,8 @@ a particular chromosome. Useful to create a small but fully functional
EnsEMBL db (e.g. laptop mini-mirror)
=cut
+use strict;
+
use Bio::EnsEMBL::DBLoader;
use Getopt::Long;
@@ -64,7 +66,7 @@ if ($lim) {
}
my $locator = "$module/host=$host;port=;dbname=$dbname;user=$dbuser;pass=$dbpass";
-$db = Bio::EnsEMBL::DBLoader->new($locator);
+my $db = Bio::EnsEMBL::DBLoader->new($locator);
$db->{RaiseError}++; # carp as soon as something wrong
unless (-d $workdir) {
@@ -78,10 +80,10 @@ print STDERR "Dumping data from small tables needed full:\n";
my @small_tables = qw(analysis analysisprocess chromosome externalDB meta
species interpro interpro_description);
$"=' ';
-$command = "$mysqldump -u $dbuser $pass_arg -T $workdir $dbname @small_tables";
+my $command = "$mysqldump -u $dbuser $pass_arg -T $workdir $dbname @small_tables";
system ($command) && die "``$command'' exited with exit status $?";
-my $command = "rm $workdir/*.sql";
+$command = "rm $workdir/*.sql";
system ($command) && die "``$command'' exited with exit status $?";
#Dump schema
@@ -100,6 +102,18 @@ my ($chrom) = $sth->fetchrow_array;
$sth = $db->prepare("select * from map_density where chrname = '$chr' into outfile '$workdir/map_density.txt'");
$sth->execute;
+warn "Finding markers for chromosome $chr\n";
+my $q = "select * from contig_landmarkMarker where chr_name = '$chr'";
+$sth= $db->prepare($q);
+$sth->execute;
+open (FILE,">$workdir/contig_landmarkMarker.txt") || die "";
+while( (my $arr = $sth->fetchrow_arrayref()) ) {
+ my @array = @$arr;
+ print FILE join("\t",@array)."\n";
+}
+close (FILE);
+
+
print STDERR "Finding golden path contigs for chromosome $chr\n";
my $golden_path_q = "select * from static_golden_path where chr_name = '$chr' $limit";
$sth = $db->prepare($golden_path_q);
@@ -118,7 +132,6 @@ close (FILE);
die "no contigs found for ``$golden_path_q''" unless @contig_ids;
my $contig_list = &get_inlist(0,@contig_ids);
-$contig_list = &get_inlist(0,@contig_ids) if @contigs;
$sth = $db->prepare("select * from contig where internal_id in $contig_list");
$sth->execute;
@@ -135,6 +148,7 @@ while( (my $arr = $sth->fetchrow_arrayref()) ) {
print FILE join("\t",@array)."\n";
}
close (FILE);
+
my $dna_list = &get_inlist(0,@dna_ids);
@clone_ids = &unique(@clone_ids);
my $clone_list = &get_inlist(0,@clone_ids);
--
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