out of date

scripts/make_db_flatfiles

-#!/usr/local/bin/perl
-
-BEGIN {
-    unshift(@INC,"../ensembl/modules");
-    unshift(@INC,"../bioperl-live");
-}
-
-use Bio::EnsEMBL::DBLoader;
-use Bio::EnsEMBL::DBSQL::Obj;
-use Bio::EnsEMBL::EMBL_Dump;
-use strict;
-use Bio::EnsEMBL::Utils::Eprof qw( eprof_start eprof_end eprof_dump);
-
-
-
-
-my $dbuser = 'ensro';
-my $dbname = 'ensembl080';
-#my $host = 'obi-wan';
-#my $host = 'cgisrv4';
-my $host = 'ensrv1';
-my $dbpass = undef;
-
-sub get_locator {
-    return "Bio::EnsEMBL::DBSQL::Obj/host=$host;dbname=$dbname;user=$dbuser;pass=$dbpass";
-}
-
-$|=1;
-
-my $outpath = '/mysql/dumps/';
-my @clones = ();
-my @contigs;
-my $db;
-my $count = 0;
-
-eval {
-    my $locator = get_locator();
-    $db =  Bio::EnsEMBL::DBLoader->new($locator);
-};
-
-if( $@ ) {
-    print STDERR "Apologies. An exception occured: $@\n";
-    exit;
-}
-
- 
-@clones = &find_clones($db);
- 
-
-
-
-
-if ($ARGV[1] =~ /start=(.*)/){
-    while ($clones[0] ne $1){
-        shift(@clones);
-    }
-}
-
-for (0..7){ shift @clones;}
-
-my $num = scalar @clones;
-print STDERR "Writing flat files for $num clones...\n";
-
-die "No clones!\n" unless (@clones);
-
-
-
-my $emblout;
-my ($clone,$as);
-
-HOP: foreach my $c (@clones){
-	$count++;
-
-	
-
-#&eprof_dump(\*STDERR);	
-
-	eval{
-	    $clone = $db->get_Clone($c);
-            $as    = $clone->virtualcontig;	    
-	};
-
-	if ($@){
-	   print STDERR "Exception in embldump for $c!: $@\n";
-	   next;
-	}
-
-	eval{
-	    &eprof_start('make_db_flatfiles - genbank');
-	    my $filename = "$outpath/genbank/$c.genbank";
-	    print STDERR "Creating genbank dump file $count: $filename...\n";
-	    open (FLAT, ">$filename") or die "Cannot create flat file ($filename): $!\n";
-	    
-	    &eprof_start('make_db_flatfiles - add_comments'); 
-           &Bio::EnsEMBL::EMBL_Dump::add_ensembl_comments($as);
-	    &eprof_end('make_db_flatfiles - add_comments');           
-
-	    &eprof_start('make_db_flatfiles - bio_seq'); 
-	    my $gbout = Bio::SeqIO->new( '-format' => 'GenBank', -fh => \*FLAT);
-	    &eprof_end('make_db_flatfiles - bio_seq');  
-
-	    &eprof_start('make_db_flatfiles - ensembl_dump'); 
-            &Bio::EnsEMBL::EMBL_Dump::ensembl_annseq_output($gbout);
-	    &eprof_end('make_db_flatfiles - ensembl_dump'); 
-
-            # genbank format - the ID line is wrong. Fall back to locus
-	    #$gbout->_id_generation_func(undef);
-	    #$gbout->_ac_generation_func(undef);
-            #$as->accession($clone->id());
-            #$as->division("PRI");
-
-	    &eprof_start('make_db_flatfiles - write_seq'); 
-            
-	    $gbout->write_seq($as);
-	    &eprof_end('make_db_flatfiles - write_seq'); 
-
-
-	    close(FLAT);
-
-	    &eprof_end('make_db_flatfiles - genbank');
-
-	    my $filename = "$outpath/embl/$c.embl";
-	    print STDERR "Creating embldump file $count: $filename...\n";
-	    open (FLAT, ">$filename") or die "Cannot create flat file ($filename): $!\n";           
-            my $emblout = Bio::SeqIO->new( '-format' => 'EMBL', -fh => \*FLAT);
-            &Bio::EnsEMBL::EMBL_Dump::ensembl_annseq_output($emblout);
-            $emblout->write_seq($as);
-
-	    close(FLAT);
-	};
-
-	if ($@){
-	   print STDERR "Exception in embldump for $c!: $@\n";
-	   next;
-	}
-}
-
-1;
-
-############################################################################
-
-sub find_clones {
-
-    my ($db) = @_;
-    my @clones;
-    my $sql = "";
-
-    if ($ARGV[0] eq 'all'){
-	$sql = "select id from clone";
-    }
-    elsif ($ARGV[0] =~ /clone=(.*)/){
-	$sql = "select id from clone where id= '$1'";
-    }
-    else{
-	$sql = "select id from clone where stored>'2000-05-04 17:22:05'";
-    }
-
-    my $sth = $db->prepare("$sql");
-    my $rv = $sth->execute();
-
-    while (my $row = $sth->fetchrow) {
-        push (@clones,$row);
-    }
-
-    return @clones;
-}
-
-############################################################################
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