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Commit 5e54877a authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Remove old unused script.

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sql/transfer_misc_affy.pl deleted 100644 → 0
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− 231
View file @ a6de3cdb
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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