relocated to website/archive folder

[jabaws.git] / binaries / linux_x86 / fasta34 / nr_to_sql.pl

diff --git a/binaries/linux_x86/fasta34/nr_to_sql.pl b/binaries/linux_x86/fasta34/nr_to_sql.pl
deleted file mode 100644 (file)
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";
-
-
-