load_KAAS.pl

#!/usr/bin/perl

use Getopt::Std;
use DBI;
use strict;
use lib $ENV{SCRIPTS};
use ENV;

my %arg;
&getopts('D:u:p:i:', \%arg);

my $user = $arg{'u'};
my $password = $arg{'p'};
my $db = $arg{'D'};
my $host = $ENV{DBSERVER} ? $ENV{DBSERVER} : 'localhost';
my $dbh = DBI->connect("dbi:mysql:host=$host;database=$db", $user, $password);
if (! $dbh) { die "Couldn't connect with $host / $db / $user / $password\n";}

my $infile = $arg{'i'};
if (! $infile) { die "No KAAS file provided with -i\n";}
if (! -r $infile) { die "$infile is not readable: $!\n";}

open my $in, $infile or die "Can't open $infile: $!\n";

while (my $line = <$in>) {
    chomp $line;
    my ($acc, $ko) = split/\s+/, $line;
    next if (! $ko);
    my @acc = split/\|/, $acc;
    my $fid = &get_feature_id_by_accession($dbh, $acc[0]);

    my $len = &get_feature_product_length($dbh, $fid);
    my $ev_i = "INSERT INTO feature_evidence (feature_id, ev_accession, feat_min, feat_max, ev_type, program)"
	. " VALUES ($fid, \"$ko\", 1, $len, \"KO\", \"KAAS\")\n";

    $dbh->do($ev_i);
}

sub get_feature_product_length {
    my $dbh = shift;
    my $fid = shift;
    my $fq = "SELECT length(product) FROM sequence_features WHERE feature_id=$fid";
    my @l = $dbh->selectrow_array($fq);
    if ($l[0]==0) {
	my $mq = "SELECT (feat_max - feat_min + 1)/3 from seq_feat_mappings m where feature_id=$fid";
	@l = $dbh->selectrow_array($mq);
    }
    return $l[0];
}