diff --git a/misc-scripts/link_out/README b/misc-scripts/link_out/README
deleted file mode 100644
index aa3a0f409c03c5c094c9420be6fbf1b7a90b64a1..0000000000000000000000000000000000000000
--- a/misc-scripts/link_out/README
+++ /dev/null
@@ -1,43 +0,0 @@
-For each release regenerate resource files by running script generate_LinkOut.pl :
-
- perl generate_LinkOut.pl -dbpattern 'core_67' -config_file linkOut_config.txt
-
-Upload new resource files to NCBI:
-
-It's best to do it on the first day of the release. NCBI links are regenerated every day based on the resource files in each provider’s directory.
-
-Host: ftp-private.ncbi.nlm.nih.gov
-Username: ensem
-Password: xxxx - check confluence page for full instructions and password: http://www.ebi.ac.uk/seqdb/confluence/display/ENS/NCBI+LinkOut+files
-
-Instructions:
-http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Transferring_Files_via_FTP
-
-From a standard ftp client:
-
-1.
-At a command prompt type: ftp ftp-private.ncbi.nlm.nih.gov and press enter.
-
-2.
-Type your login name at the login prompt and press enter. (See how to obtain ftp account from NCBI.)
-
-3.
-Type your password at the password prompt and press enter.
-
-4.
-You should now be logged into the ftp server. If you receive an error message, check your login information, type 'bye' followed by enter, and retry steps 1-3.
-
-5.
-Type 'bin' and press enter. This changes your ftp server to BINARY mode.
-
-6.
-Type ‘cd holdings’ and press enter. This changes your current directory.
-
-7.
-Type the 'put' command, followed by your pathname or drive and filename and press enter. (For example, 'put C:\filename' or 'put /home/testfiles/journalv6n3'.)
-
-8.
-Type 'dir' and press enter to display the files in the current directory.
-
-9.
-Type 'bye' to disconnect from the server and close the ftp session.
diff --git a/misc-scripts/link_out/generate_LinkOut.pl b/misc-scripts/link_out/generate_LinkOut.pl
deleted file mode 100644
index dc9d6a5c6ffb0ecf5b2552ba3008c2b9fd334d08..0000000000000000000000000000000000000000
--- a/misc-scripts/link_out/generate_LinkOut.pl
+++ /dev/null
@@ -1,228 +0,0 @@
-# Generate LinkOut resource file for NCBI website.
-# Author: Monika Komorowska
-# Date : 06.04.2011
-
-
-use strict;
-use DBI;
-use Getopt::Long;
-
-sub new_file;
-
-my ( $dbpattern, $out_file, $config_file );
-
-GetOptions( "dbpattern|pattern=s", \$dbpattern,
- "out_file=s", \$out_file,
- "config_file=s", \$config_file,
- );
-
-if( !$dbpattern ) {
- usage();
-}
-
-if (!$config_file) {
- $config_file = "linkOut_config.txt";
-}
-
-open( CFH, "<$config_file" ) or die("Can't open $config_file\n");
-my @hosts;
-while (my $line = <CFH>) {
- push( @hosts, $line);
-}
-close CFH;
-
-#delete the old resource files
-if (-e "resources*") {
- exec("rm -r resources*");
-}
-
-if( !$out_file ) {
- $out_file = "resources";
-}
-
-my $file_size;
-my $number_of_files = 1;
-
-my $header = <<HEADER;
-<?xml version="1.0"?>
-<!DOCTYPE LinkSet PUBLIC "-//NLM//DTD LinkOut 1.0//EN"
-"http://www.ncbi.nlm.nih.gov/entrez/linkout/doc/LinkOut.dtd"
-[<!ENTITY base.url "http://www.ensembl.org/id/">]>
-
-<LinkSet>
-HEADER
-
-my $header_size;
-{
- use bytes;
- $header_size = length($header);
-}
-
-new_file();
-my $link_no = 0;
-
-foreach my $host_line (@hosts) {
- $host_line =~ /([^\s]+)\s+([^\s]+)\s*(\d*)/;
- my $host = $1;
- my $user = $2;
- my $port = $3;
-
- my $dsn = "DBI:mysql:host=$host";
- if( $port =~ /\d+/) {
- $dsn .= ";port=$port";
- }
- my $db = DBI->connect( $dsn, $user);
- if (!defined $db) {
- my $message = "Can't connect to host: $host, port: ";
- if($port =~ /\d+/) {
- $message .= $port;
- } else {
- $message .= 'default';
- }
- $message .= ", user: $user\n";
- print STDOUT $message;
- next;
- }
-
- my @dbnames = map {$_->[0] } @{ $db->selectall_arrayref( "show databases" ) };
-
- for my $dbname ( @dbnames ) {
- if( $dbpattern ) {
- if( $dbname !~ /$dbpattern/ ) {
- next;
- }
- }
-
- $db->do( "use $dbname" );
- #get nucleotide data
- my ($entrez_db, $ref_seq_accession,$ensembl_stable_id);
- my $current_file_no = $number_of_files;
- $entrez_db = "Nucleotide";
-
- my $sth = $db->prepare("SELECT dbprimary_acc, stable_id FROM object_xref o INNER JOIN xref x on o.xref_id = x.xref_id INNER JOIN external_db e on e.external_db_id =x.external_db_id INNER JOIN transcript on ensembl_id = transcript_id WHERE db_name in ('RefSeq_dna', 'RefSeq_dna_predicted', 'RefSeq_mRNA', 'RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted') GROUP BY dbprimary_acc, stable_id");
- $sth->execute();
- print STDOUT "Writing out nucleotide links for database $dbname\n";
- my $nucleotide_links = 0;
- while ( ($ref_seq_accession,$ensembl_stable_id) = $sth->fetchrow_array() )
- {
- $link_no ++;
-my $link = " <Link>
- <LinkId>$link_no</LinkId>
- <ProviderId>7853</ProviderId>
- <ObjectSelector>
- <Database>$entrez_db</Database>
- <ObjectList>
- <Query>$ref_seq_accession</Query>
- </ObjectList>
- </ObjectSelector>
- <ObjectUrl>
- <Base>&base.url;</Base>
- <Rule>$ensembl_stable_id</Rule>
- </ObjectUrl>
- </Link>\n";
- {
- use bytes;
- my $byte_size = length($link);
- $file_size += $byte_size;
- }
- #each file has a limit of 20Mb
- if ($file_size >= 19900000) {
- $number_of_files ++;
- new_file();
- }
- print FH $link;
- $nucleotide_links ++;
- }
-
- $sth->finish();
- my $message = "Written out $nucleotide_links nucleotide links for database $dbname";
- if ($nucleotide_links > 0) {
- $message .= " in file(s):\n";
- for (my $i = $current_file_no; $i <= $number_of_files; $i++) {
- $message .= $out_file . "_" . "$i\n";
- }
- } else {
- $message .= "\n";
- }
- print STDOUT $message;
-
- #get protein data
- $current_file_no = $number_of_files;
- $entrez_db = "Protein";
- $sth = $db->prepare("SELECT dbprimary_acc, stable_id FROM object_xref o INNER JOIN xref x on o.xref_id = x.xref_id INNER JOIN external_db e on e.external_db_id =x.external_db_id INNER JOIN translation on ensembl_id = translation_id WHERE db_name in ('RefSeq_peptide', 'RefSeq_peptide_predicted') group by dbprimary_acc, stable_id");
- $sth->execute();
- print STDOUT "Writing out protein links for database $dbname\n";
- my $protein_links = 0;
- while ( ($ref_seq_accession,$ensembl_stable_id) = $sth->fetchrow_array() )
- {
- $link_no ++;
-my $link = " <Link>
- <LinkId>$link_no</LinkId>
- <ProviderId>7853</ProviderId>
- <ObjectSelector>
- <Database>$entrez_db</Database>
- <ObjectList>
- <Query>$ref_seq_accession</Query>
- </ObjectList>
- </ObjectSelector>
- <ObjectUrl>
- <Base>&base.url;</Base>
- <Rule>$ensembl_stable_id</Rule>
- </ObjectUrl>
- </Link>\n";
- {
- use bytes;
- my $byte_size = length($link);
- $file_size += $byte_size;
- }
- #each file has a limit of 20Mb
- if ($file_size >= 19900000) {
- $number_of_files ++;
- new_file();
- }
- print FH $link;
- $protein_links ++;
- }
-
- $sth->finish();
- $message = "Written out $protein_links protein links for database $dbname";
- if ($protein_links > 0) {
- $message .= " in file(s):\n";
- for (my $i = $current_file_no; $i <= $number_of_files; $i++) {
- $message .= $out_file . "$i\n";
- }
- } else {
- $message .= "\n";
- }
- print STDOUT $message;
- }
-
- $db->disconnect();
- print FH "</LinkSet>";
- close FH;
-}
-sub usage {
- print STDERR <<EOF
-
- Usage: generate_LinkOut options
- -dbpattern database name pattern
- -out_file output resource file name, default 'resources'
- -config_file should contain one or more lines with: host user port(optional), e.g. ens-staging1 ensro
-EOF
-;
- exit;
-}
-
-sub new_file
-{
- if ($number_of_files > 1) {
- print FH "</LinkSet>";
- close FH;
- }
- my $file_name = $out_file . $number_of_files . '.xml';
- open( FH, ">$file_name" ) or die("Can't open $file_name\n");
- print FH $header;
- $file_size = $header_size;
-}
-
-
diff --git a/misc-scripts/link_out/linkOut_config.txt b/misc-scripts/link_out/linkOut_config.txt
deleted file mode 100644
index 6d0bb9e41f9903f05a3c7b95a16a2873e05a3022..0000000000000000000000000000000000000000
--- a/misc-scripts/link_out/linkOut_config.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-ens-staging1 ensro
-ens-staging2 ensro