alignDB.pl

#!/usr/bin/env perl
use strict;
use warnings;
use autodie;

use Getopt::Long qw();
use Config::Tiny;
use FindBin;
use YAML::Syck qw();

use AlignDB::IntSpan;
use AlignDB::Stopwatch;

#----------------------------------------------------------#
# GetOpt section
#----------------------------------------------------------#
my $conf = Config::Tiny->read("$FindBin::RealBin/alignDB.ini");

# record ARGV and Config
my $stopwatch = AlignDB::Stopwatch->new;

=head1 NAME

alignDB.pl - Batch process multi-way alignDB with/without outgroup

=cut

Getopt::Long::GetOptions(
    'help|?'         => sub { Getopt::Long::HelpMessage(0) },
    'server|s=s'     => \( my $server = $conf->{database}{server} ),
    'port=i'         => \( my $port = $conf->{database}{port} ),
    'db|d=s'         => \( my $db_name = $conf->{database}{db} ),
    'username|u=s'   => \( my $username = $conf->{database}{username} ),
    'password|p=s'   => \( my $password = $conf->{database}{password} ),
    'ensembl|e=s'    => \( my $ensembl_db = $conf->{database}{ensembl} ),
    'dir_align|da=s' => \( my $dir_align = $conf->{generate}{dir_align} ),
    'chr=s'          => \( my $init_chr = $conf->{generate}{file_chr_length} ),
    'annotation|a=s' => \( my $file_anno = $conf->{generate}{file_anno} ),
    'parallel=i'     => \( my $parallel = $conf->{generate}{parallel} ),
    'batch=i'        => \( my $batch_number = $conf->{generate}{batch} ),
    'length|lt=i'    => \( my $length = $conf->{generate}{length} ),
    'outgroup|o'     => \( my $outgroup ),
    'run|r=s'        => \( my $run = "common" ),
) or Getopt::Long::HelpMessage(1);

# prepare to run tasks in @tasks
my @tasks;
if ( $run eq 'gui' ) {
    @tasks = (0);
}
elsif ( $run eq 'all' ) {
    @tasks = ( 1 .. 45 );
}
elsif ( $run eq 'skeleton' ) {
    @tasks = ( 1 .. 3 );
}
elsif ( $run eq 'basic' ) {
    @tasks = ( 1 .. 5, 40 );
}
elsif ( $run eq 'common' ) {
    @tasks = ( 1 .. 5, 21, 30, 31, 40, 41, 44 );
}
elsif ( $run eq 'gc' ) {
    @tasks = ( 1 .. 5, 10, 21, 30, 31, 40 .. 42 );
}
elsif ( $run eq 'gene' ) {
    @tasks = ( 1 .. 5, 10, 20, 21, 30 .. 33, 40 .. 44 );
}
elsif ( $run eq 'stat' ) {
    @tasks = ( 40 .. 44 );
}
else {
    $run =~ s/\"\'//s;
    if ( AlignDB::IntSpan->valid($run) ) {
        my $set = AlignDB::IntSpan->new($run);
        @tasks = $set->elements;
    }
    else {
        @tasks = grep {/\d/} split /\s/, $run;
    }
}

#----------------------------------------------------------#
# dispatch table
#----------------------------------------------------------#
my $dispatch = {
    0 => "perl $FindBin::RealBin/gui/gui3.pl",
    1 => "perl $FindBin::RealBin/init/init_alignDB.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . ( $init_chr ? " --chr $init_chr" : "" ),
    2 => "perl $FindBin::RealBin/init/gen_alignDB.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " --da $dir_align"
        . " --lt $length"
        . " --parallel $parallel"
        . ( $outgroup ? " --outgroup" : "" ),
    3 => undef,
    5 => "perl $FindBin::RealBin/init/insert_isw.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " --parallel $parallel"
        . " --batch $batch_number"
        . ( $outgroup ? " --outgroup" : "" ),
    10 => "perl $FindBin::RealBin/init/insert_gc.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " --parallel $parallel"
        . " --batch $batch_number",
    20 => "perl $FindBin::RealBin/init/insert_gene.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " -e $ensembl_db"
        . " --parallel $parallel",
    21 => "perl $FindBin::RealBin/init/update_sw_cv.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " --parallel $parallel"
        . " --batch $batch_number",
    30 => "perl $FindBin::RealBin/init/update_annotation.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " -a $file_anno"
        . " --parallel $parallel"
        . " --batch $batch_number",
    31 => "perl $FindBin::RealBin/init/update_indel_slippage.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name",
    33 => "perl $FindBin::RealBin/init/update_snp_dnds.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name",
    40 => "perl $FindBin::RealBin/stat/common_stat_factory.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " --index --chart"
        . " -o $db_name.common.xlsx",
    41 => "perl $FindBin::RealBin/stat/multi_stat_factory.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " --index --chart"
        . " -o $db_name.multi.xlsx",
    42 => "perl $FindBin::RealBin/stat/gc_stat_factory.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " --index --chart"
        . " -o $db_name.gc.xlsx",
    43 => "perl $FindBin::RealBin/stat/gene_stat_factory.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " --index --chart"
        . " -o $db_name.gene.xlsx",
    44 => "perl $FindBin::RealBin/stat/mvar_stat_factory.pl"
        . " -s $server"
        . " --port $port"
        . " -u $username"
        . " --password $password"
        . " -d $db_name"
        . " -o $db_name.mvar.xlsx",
};

#----------------------------#
# Run
#----------------------------#

for my $step (@tasks) {

    # use the dispatch template to generate $cmd
    my $cmd = $dispatch->{$step};
    next unless $cmd;

    if ( $step == 30 and !defined $file_anno ) {
        next;
    }

    $stopwatch->block_message("Processing Step $step");
    $stopwatch->block_message($cmd);
    system $cmd;
    $stopwatch->block_message("Finish Step $step");
}

print "\n";

$stopwatch->end_message;
exit;

__END__