From f88c96ae83875a87603aa79d333a2ab2738e5adb Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 9 Jan 2004 14:15:14 +0000
Subject: [PATCH] out of date
---
scripts/make_db_flatfiles | 177 --------------------------------------
1 file changed, 177 deletions(-)
delete mode 100755 scripts/make_db_flatfiles
diff --git a/scripts/make_db_flatfiles b/scripts/make_db_flatfiles
deleted file mode 100755
index 6891200d01..0000000000
--- a/scripts/make_db_flatfiles
+++ /dev/null
@@ -1,177 +0,0 @@
-#!/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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