Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / fasta34 / nr_to_sql.pl

diff --git a/website/archive/binaries/mac/src/fasta34/nr_to_sql.pl b/website/archive/binaries/mac/src/fasta34/nr_to_sql.pl
new file mode 100644 (file)
index 0000000..9828de6
--- /dev/null
+++ b/website/archive/binaries/mac/src/fasta34/nr_to_sql.pl
@@ -0,0 +1,86 @@
+#!/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";
+
+
+