removed very old script

misc-scripts/mouse_reads/features_from_cigar.pl

-
-# This script takes as argument the name of a gzipped cigar file, 
-# which contains exonerate result from mouse traces to human dna
-
-# you have to provide an empty ensembl database with just contig table 
-# filled 
-# lots of empty diskspace
-# change db deatils below !!
-
-
-
-use DBI;
-
-# only use with local host!
-my $file = shift;
-
-my $dsn = "DBI:mysql:database=mouse_jun_hum_apr_arne;host=localhost";
-my $dbh = DBI->connect($dsn,'root');
-my $tmpfile = "/scratch1/ensembl/arne/mouse_features.txt";
-
-
-
-
-open( EXONERATE, "gzip -dc $file|" ) or die( "cant open exonerate cigar line file" );
-open( TMP, ">$tmpfile" ) or die ("cant open tmpfile $tmpfile");
-
-# print join( "\t", contig, seq_start, seq_end, score, strand, analysis, "exonerate_gapped", hstart, hend, hid )
-
-$sth = $dbh->prepare( "select internal_id, id from contig" );
-
-my ( $internal, $external );
-$sth->execute();
-$sth->bind_columns( \$internal, \$external );
-
-while( $sth->fetch() ) {
-  $contigHash{$external} = $internal;
-}
-
-my $count = 0;
-
-while( <EXONERATE> ) {
-  chomp;
-  split;
-  ($hid) = $_[2] =~ /(.*)-[0-9]*$/;
-  $hstart = $_[3]+1;
-  $hend = $_[4];
-  $strand = ($_[5] eq '-') ? -1 : 1;
-  $contig = $contigHash{$_[6]};
-  $seq_start = $_[7]+1;
-  $seq_end = $_[8];
-  $score = $_[10];
-  $analysis = 1;
-
-  print TMP ( join( "\t",( $contig, $seq_start, $seq_end, $score, 
-			   $strand, $analysis, "exonerate_gapped", 
-			   $hstart, $hend, $hid )), "\n" );
-  $count++;
-  if( $count % 100000 == 0 ) {
-    print STDERR ".";
-#    exit;
-  }
-}
-
-
-$dbh->do( "load data infile '$tmpfile' into table feature( contig, seq_start, seq_end, score, strand, analysis, name, hstart, hend, hid )" );
-$dbh->do( "insert into analysis( id, db, db_version, program, program_version, gff_source, gff_feature) values( 1, \"exonerate_gapped\", \"\", \"exonerate\", \"1\", \"exonerate_gapped\", \"similarity\" )" );
-$dbh->disconnect();
-
-exit;
-
-  
-# algorithm		     
-
-# build contig internal hash
-# read cigar lines from gzip -dc pipe
-# print feature lines into tmpfile
-
-# issue load data infile command .
-# fill in one row in analysis table..
-