From 5e54877a1bf01938a93b61d3926d6b1aaefaf1a1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 1 Sep 2011 12:25:09 +0000
Subject: [PATCH] Remove old unused script.
---
sql/transfer_misc_affy.pl | 231 --------------------------------------
1 file changed, 231 deletions(-)
delete mode 100644 sql/transfer_misc_affy.pl
diff --git a/sql/transfer_misc_affy.pl b/sql/transfer_misc_affy.pl
deleted file mode 100644
index fa6a489d86..0000000000
--- a/sql/transfer_misc_affy.pl
+++ /dev/null
@@ -1,231 +0,0 @@
-use strict;
-use warnings;
-use Getopt::Long;
-use Data::Dumper;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-
-my $dbCore;
-my $tmp_dir; #tmp directory to store the dumps of the data, by default /ecs2/scratch3/dani
-my $affy_array; #hash containing the relation between misc_set_id => affy_array_id
-my $probe_feature; #hash containing the information relevant to the affy_feature table
-my $affy_probe; #hash containing the information relevant to the affy_probe table: misc_set_id -> [probeset,probename]
-my $affy_probe_id = 1; #first affy_probe_id in the affy_probe table
-
-# unbeknown to me there are actually probesets that contain the same probe twice.
-# for the conversion we have to take them out, it will work better when the features
-# and probes are generate from the fasta files directly
-
-my %kill_probeset = ( '892_at' => 1 );
-
-
-{
- my ($chost, $cuser, $cpass, $cport, $cdbname); #ensembl core db
- GetOptions('host=s' => \$chost,
- 'user=s' => \$cuser,
- 'pass=s' => \$cpass,
- 'port=i' => \$cport,
- 'dbname=s' => \$cdbname,
- 'tmpdir=s' => \$tmp_dir
- );
- #by default, connect to the stagging server at ecs2:3364
- $chost ||= 'ecs2';
- $cuser ||= 'ensadmin';
- $cport ||= 3364;
-
- $tmp_dir ||= '/ecs2/scratch3/dani';
-
- usage('-cdbname argument is required.') if(!$cdbname);
- #connection to the Core database
- $dbCore = Bio::EnsEMBL::DBSQL::DBAdaptor->new
- (-host => $chost,
- -user => $cuser,
- -pass => $cpass,
- -port => $cport,
- -dbname => $cdbname);
-
-}
-
-&populate_affy_array($dbCore);
-print STDERR "Populated affy_array table\n";
-&populate_probe_info($dbCore);
-
-#get all the data from the misc_set table and copy it to the affy array table
-sub populate_affy_array{
- my $dbCore = shift;
- my $affy_name;
- my $misc_set_id;
- my $sth = $dbCore->dbc()->prepare(qq{SELECT misc_set_id,name from misc_set where code like 'AFFY%'
- });
- my $sth_insert = $dbCore->dbc()->prepare(qq{INSERT INTO affy_array (name) VALUES (?)
- }
- );
- $sth->execute();
- $sth->bind_columns(\$misc_set_id,\$affy_name);
- #copy each entry in the affy_array table and keep the affy_array_id assigned for a later use
- while ($sth->fetch){
- $sth_insert->execute($affy_name);
- $affy_array->{$misc_set_id} = $dbCore->dbc()->db_handle()->{'mysql_insertid'};
- }
- $sth->finish;
-}
-
-sub populate_probe_info{
- my $dbCore = shift;
-
- my ($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand,
- $misc_set_id, $complete_probename, $mismatch);
-
- my ($affy_name, $affy_probeset, $probename);
-
- my $previous_seq_region_id = -1;
- my $previous_seq_region_start = -1;
- my $old_affy_probe;
- my $probe_set;
- print STDERR "Going to get affy information....\n";
-
-
- my $sql =
- qq{
- SELECT STRAIGHT_JOIN seq_region_id, seq_region_start, seq_region_end,
- seq_region_strand, mff.misc_set_id, ma1.value,
- (IF (ma2.value = 'Mismatch',1,0)) as mismatch
- FROM misc_feature mf, misc_attrib ma1, misc_attrib ma2,
- misc_feature_misc_set mff, attrib_type at1,
- attrib_type at2, misc_set ms
- WHERE ma2.misc_feature_id = mf.misc_feature_id
- AND ma2.attrib_type_id = at2.attrib_type_id
- AND at2.code = 'matchStatus'
- AND ma1.attrib_type_id = at1.attrib_type_id
- AND at1.code = 'probeName'
- AND ma1.misc_feature_id = mf.misc_feature_id
- AND mf.misc_feature_id = mff.misc_feature_id
- AND ms.misc_set_id = mff.misc_set_id
- AND ms.code <> 'All_Affy'
- ORDER BY seq_region_id,seq_region_start };
-
-
- print STDERR "Ready to create affy files\n";
- open FEATURE, ">$tmp_dir/affy_feature_$$\.txt";
- open PROBE, ">$tmp_dir/affy_probe_$$\.txt";
-
- my %stored_probes;
- my $current_probe_id = 1;
- my %merge_cache;
- my $merge_key;
-
- # merging of probes is only allowes for mismatch = 0
- for my $mismatch_process ( 0..1 ) {
- my $sth = $dbCore->dbc()->prepare( $sql );
- $sth->{mysql_use_result} = 1;
- $sth->execute();
- $sth->bind_columns(\$seq_region_id, \$seq_region_start, \$seq_region_end,
- \$seq_region_strand,
- \$misc_set_id, \$complete_probename, \$mismatch);
-
-
- my $prev_seq_region_id = -1;
- my $prev_start = -1;
-
- while($sth->fetch()){
-
- next unless( $mismatch == $mismatch_process );
-
- # flush the merge cache regularly
- if( $prev_start != $seq_region_start ||
- $prev_seq_region_id != $seq_region_id ) {
- %merge_cache = ();
- $prev_start = $seq_region_start;
- $prev_seq_region_id = $seq_region_id;
- }
-
- my ($affy_name,$affy_probeset,$probename) = split /:/,$complete_probename,3;
- if( $kill_probeset{ $affy_probeset } ) { next; }
-
- # first check wether we have to store probe information
- my $probe_id = $stored_probes{ $complete_probename };
- if( ! $mismatch ) {
- $merge_key = join( "-", $seq_region_id, $seq_region_start, $seq_region_end,
- $seq_region_strand, $mismatch, $affy_probeset );
- }
-
- if( ! defined $probe_id ) {
- # probe information needs to be stored, but new probe_id or existing one?
- $probe_id = $merge_cache{ $merge_key };
- if(( ! defined $probe_id ) || $mismatch ) {
- $probe_id = $current_probe_id++;
- }
-
- print PROBE join( "\t", $probe_id,
- $affy_array->{$misc_set_id},
- $affy_probeset,
- $probename),"\n";
- $stored_probes{ $complete_probename } = $probe_id;
- }
- # at this point the probe_id is correct, it might already be clear that the
- # feature doesnt need storing (there is already a merge cache entry for
- # this position.
-
-
- # do we want to store the feature ?
- # if its already stored with that probe_id its in the
- # merge_cache no addition feature is needed
- if( $mismatch ) {
- $merge_key = join( "-", $probe_id, $seq_region_id, $seq_region_start, $seq_region_end,
- $seq_region_strand );
- }
-
- if( exists $merge_cache{ $merge_key } ) {
- # this one is already stored
- } else {
- $merge_cache{ $merge_key } = $probe_id;
- print FEATURE join ("\t",$seq_region_id, $seq_region_start,
- $seq_region_end, $seq_region_strand,
- $mismatch, $probe_id ),"\n";
- }
- }
-
- $sth->finish();
- }
-
- close FEATURE;
- close PROBE;
-
- #and finally import the information
- print STDERR "Loading new affy information\n";
- load($dbCore,"$tmp_dir/affy_feature_$$\.txt",qw(affy_feature seq_region_id seq_region_start seq_region_end seq_region_strand mismatches affy_probe_id));
- load($dbCore,"$tmp_dir/affy_probe_$$\.txt",qw(affy_probe affy_probe_id affy_array_id probeset name));
-}
-
-
-sub load{
- my $dbCore = shift;
- my $file = shift;
- my $tablename = shift;
- my @colnames = @_;
-
- my $cols = join( ",", @colnames );
- my $sql = qq{
- LOAD DATA INFILE '$file'
- INTO TABLE $tablename ($cols)
- };
- $dbCore->dbc()->do($sql);
- unlink ("$file");
-}
-
-sub usage {
- my $msg = shift;
-
- print STDERR <<EOF;
-
- usage: perl affy_data.pl <options>
-
- options:
- -chost <hostname> hostname of core Ensembl MySQL database (default = ecs2)
- -cuser <user> username of core Ensembl MySQL database (default = ensadmin)
- -cpass <pass> password of core Ensembl MySQL database
- -cport <port> TCP port of core Ensembl MySQL database (default = 3364)
- -cdbname <dbname> dbname of core Ensembl MySQL database
-EOF
-
- die("\n$msg\n\n");
-}
--
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