Script to add mouse knockouts to the simple features

misc-scripts/mouse_knockouts/add_ikmc_as_simple_features.pl

+#!/usr/local/ensembl/bin/perl -w
+
+#
+# updates the external db tables on all of the core databases on a given host
+#
+
+use strict;
+
+use Getopt::Long;
+use DBI;
+use IO::File;
+
+my ( $host, $user, $pass,   $port, $dbname, $file);
+
+GetOptions( "dbhost|host=s",        \$host,
+            "dbuser|user=s",        \$user,
+            "dbpass|pass=s",        \$pass,
+            "dbport|port=i",        \$port,
+            "file=s",        \$file,
+            "dbname=s",    \$dbname);
+
+$port ||= 3306;
+$host ||= "ens-research";
+$dbname ||= "ianl_mus_musculus_core_58_37k";
+
+# connect to the database
+my $dsn = "DBI:mysql:host=$host;port=$port;database=$dbname";
+
+my $db = DBI->connect( $dsn, $user, $pass, {RaiseError => 1} );
+
+
+my %analysis = ("No products available yet" => 0, 
+                "ES cells available" => 0,
+                "Mice available" => 0,
+                "Vector available" => 0);
+
+# if the 4 analysis do not exist create them
+# if they do exist delete entrys in the simple feature table
+
+
+my $find_sth = $db->prepare("SELECT  analysis_id FROM analysis where logic_name like ?")|| die "Could not prepare find_sth";
+
+my $create_sth = $db->prepare("INSERT into analysis (logic_name) values (?)") || die "Could not prepare create_sth";
+
+my $delete_sth = $db->prepare("DELETE from simple_feature where analysis_id = ?" )|| die "Could not prepare delete_sth";
+
+foreach my $anal (keys %analysis){
+  my $logic_name = "IKMC_".$anal;
+  $logic_name =~ s/ /_/g;
+
+  my $id =undef;
+  $find_sth->execute($logic_name);
+  $find_sth->bind_columns(\$id);
+  $find_sth->fetch;
+  if(defined($id)){ # delete existing simple features
+    print STDERR "Analysis $logic_name already exists so clearing entrys for this ($id) in the simple_feature table\n";
+    $delete_sth->execute($id) || die "Could not delete form simple table for id = $id";
+  }
+  else{             # create analysis
+    $create_sth->execute($logic_name) || die "Could not create new analysis $logic_name";
+    $id = $create_sth->{'mysql_insertid'};
+    print STDERR "Creating new anlysis $logic_name ($id)\n";
+  }
+  $analysis{$anal} = $id;
+}
+
+$find_sth->finish();
+$create_sth->finish();
+$delete_sth->finish();
+
+
+# make a hashes for gene 
+# gene2seqregion{stable_id} = seq_region_id
+# gene2start....
+# gene2end  ....
+my %gene2seqregion;
+my %gene2start;
+my %gene2end;
+my %gene2strand;
+
+my $gene_sth = $db->prepare("SELECT  gsi.stable_id, g.seq_region_id, g.seq_region_start, g.seq_region_end, g.seq_region_strand FROM gene g, gene_stable_id gsi WHERE g.gene_id = gsi.gene_id") || die "Could not prepare gene_sth";
+
+$gene_sth->execute();
+my ($stable_id, $seq, $start, $end, $strand);
+$gene_sth->bind_columns(\$stable_id, \$seq, \$start, \$end, \$strand);
+while($gene_sth->fetch()){
+  $gene2seqregion{$stable_id} = $seq;
+  $gene2start{$stable_id}     = $start;
+  $gene2end{$stable_id}       = $end;
+  $gene2strand{$stable_id}    = $strand;
+}
+#process the file and add new simple features
+
+my $insert_sth = $db->prepare("INSERT INTO simple_feature (seq_region_id, seq_region_start, seq_region_end, seq_region_strand, display_label, analysis_id ) VALUES(?, ?, ?, ?, ?, ?)") || die "Could not prepare insert_sth";
+
+my $ikmc = get_filehandle($file);
+my %count;
+while ( $_ = $ikmc->getline() ) {
+
+  chomp;
+  my ($mgi, $label, $type, $stable_id) = split /\t/;
+
+  if((defined($stable_id) and $stable_id) and defined($gene2seqregion{$stable_id})){
+    if(!defined($analysis{$type})){
+      print STDERR $_."\nUnknown type *$type*\n";
+    }
+    else{
+      $insert_sth->execute($gene2seqregion{$stable_id}, 
+                           $gene2start{$stable_id},
+                           $gene2end{$stable_id},
+                           $gene2strand{$stable_id}, 
+                           $mgi,
+                           $analysis{$type}) || die "Could not insert new values";
+      $count{$type}++;
+    }
+  }
+  else{
+    if(!defined($stable_id) or !$stable_id){
+      $count{"no stable_id"}++;
+    }
+    else{
+      print STDERR "Could not find stable id $stable_id\n";
+    }
+  }
+}
+
+foreach my $key (keys %count){
+  print $key."\t".$count{$key}."\n";
+}
+
+
+sub get_filehandle
+{
+    my ($file_name) = @_;
+
+    my $io;
+
+    my $alt_file_name = $file_name;
+    $alt_file_name =~ s/\.(gz|Z)$//;
+
+    if ( $alt_file_name eq $file_name ) {
+        $alt_file_name .= '.gz';
+    }
+
+    if ( !-f $file_name ) {
+        carp(   "File '$file_name' does not exist, "
+              . "will try '$alt_file_name'" );
+        $file_name = $alt_file_name;
+    }
+
+    if ( $file_name =~ /\.(gz|Z)$/ ) {
+        # Read from zcat pipe
+        $io = IO::File->new("zcat $file_name |")
+          or carp("Can not open file '$file_name' with 'zcat'");
+    } else {
+        # Read file normally
+        $io = IO::File->new($file_name)
+          or carp("Can not open file '$file_name'");
+    }
+
+    if ( !defined $io ) { return undef }
+
+    print "Reading from '$file_name'...\n";
+
+    return $io;
+}