X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Flinux_x86%2Ffasta34%2Fnr_to_sql.pl;fp=binaries%2Flinux_x86%2Ffasta34%2Fnr_to_sql.pl;h=0000000000000000000000000000000000000000;hb=9d1925db13bc3ec234a35240bc1accf069270068;hp=9828de67e9daeb02b98b0fb2069b238d0a05fff0;hpb=3a91afb9d44716e39a3365a0ee3f2df41212a0e4;p=jabaws.git

diff --git a/binaries/linux_x86/fasta34/nr_to_sql.pl b/binaries/linux_x86/fasta34/nr_to_sql.pl
deleted file mode 100644
index 9828de6..0000000
--- a/binaries/linux_x86/fasta34/nr_to_sql.pl
+++ /dev/null
@@ -1,86 +0,0 @@
-#!/usr/bin/perl -w
-
-use DBI;
-
-$SIG{__WARN__} = sub { die @_ };
-
-my $mysql = DBI->connect("DBI:mysql:database=seq_demo;user=seq_demo;password=demo_pass");
-
-$mysql->do(q{LOCK TABLES prot WRITE,
-	     annot WRITE,
-	     sp WRITE });
-
-my $EL = 125;
-my $NA = 123;
-
-my @aatrans = ($EL,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$EL,$NA,$NA,$EL,$NA,$NA,
-	       $NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,
-	       $NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA, 24,$NA,$NA,$NA,$NA,$NA,
-	       $NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,
-	       $NA,  1, 21,  5,  4,  7, 14,  8,  9, 10,$NA, 12, 11, 13,  3,$NA,
-	        15,  6,  2, 16, 17,$NA, 20, 18, 23, 19, 22,$NA,$NA,$NA,$NA,$NA,
-	       $NA,  1, 21,  5,  4,  7, 14,  8,  9, 10,$NA, 12, 11, 13,  3,$NA,
-	        15,  6,  2, 16, 17,$NA, 20, 18, 23, 19, 22,$NA,$NA,$NA,$NA,$NA
-	      );
-
-my $ins_prot = $mysql->prepare(q{
-    INSERT INTO prot (seq,bin,len) VALUES (?, ?, ?)
-    });
-
-my $ins_annot = $mysql->prepare(q{
-    INSERT INTO annot (gi, prot_id, db, descr) VALUES (?, ?, ?, ?)
-    });
-
-my $ins_sp = $mysql->prepare(q{
-    INSERT INTO sp (gi, acc, name) VALUES (?, ?, ?)
-    });
-
-use vars qw( $seq $bin $tot_seq $tot_annot $tot_sp );
-use vars qw( $gi $prot_id $db $desc $sp_acc $sp_name );
-use vars qw( $header $seq @entries );
-use vars qw( $gi $db $db_acc $db_name $desc);
-
-$tot_seq = $tot_annot = $tot_sp = 0;
-
-for my $db_file ( @ARGV ) {
-    open(DATA, "<$db_file") or die $!;
-    local $/ = "\n>";
-    while (<DATA>) {
-	chomp; # remove trailing "\n>" record header
-	($header, $seq) = $_ =~ m/^>?  # record separator (first entry)
-	    ( [^\n]* ) \n  # header line
-		(     .* )     # the sequence
-		    /osx; # optimize, multiline, commented
-	
-	$seq =~ s/\W|\d//sg;
-	$bin = pack('C*', map { $aatrans[unpack('C', $_)] } split(//, $seq));
-	$ins_prot->execute($seq,$bin,length($seq));
-	$prot_id = $ins_prot->{mysql_insertid};
-
-	$tot_seq++;
-
-#	print STDERR "Inserted $prot_id: ". length($seq)."\n";
-
-	@entries = split(/\001/, $header);
-
-	for ( @entries ) {
-	    ($gi,$db,$db_acc,$db_name,$desc)= 
-		$_ =~ /^gi\|(\d+)\|([a-z]+)\|(\S*)\|(\S*) (.*)$/o;
-#	    print "$prot_id: $gi\t$db\t$db_acc\t$desc\n";
-	    $ins_annot->execute($gi,$prot_id,$db,$desc);
-
-	    $tot_annot++;
-
-	    if ($db eq "sp") {
-		$ins_sp->execute($gi,$db_acc,$db_name);
-		$tot_sp++;
-	    }
-	}
-    }
-    close(DATA);
-}
-
-print "Inserted $tot_seq sequences; $tot_annot annotations; $tot_sp swissprot\n";
-
-
-