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#!/usr/bin/perl -w
################################################################
# copyright (c) 2004, 2014 by William R. Pearson and The Rector &
# Visitors of the University of Virginia */
################################################################
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,
# software distributed under this License is distributed on an "AS
# IS" BASIS, WITHOUT WRRANTIES OR CONDITIONS OF ANY KIND, either
# express or implied. See the License for the specific language
# governing permissions and limitations under the License.
################################################################
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";
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