#!/usr/bin/perl -w

#######
# make_fastas.pl
#
my $purpose = "Extracts sequences from mast as FASTA";
# 
######## 

use strict;
use DBI;
use Dumpvalue;
use Data::Dumper;
use Term::ReadKey;
use Getopt::Long;
use Bio::Seq;
use Bio::SeqIO;

my %options = ();
GetOptions(\%options,'saskatoon|s!','saskatoonfile=s');
my $opts = &validate_options(\%options);


# create a few global variables
my $dumper = new Dumpvalue();
my $stdouth = new Bio::SeqIO(    -fh  =>   \*STDOUT,
                              -format   =>   'fasta');
my $handle;
if ($opts->{saskatoonfile}) {
     $handle = new Bio::SeqIO(     -file  =>   ">".$opts->{saskatoonfile},
                                        -format   =>   'fasta');
}
else {
     $handle = $stdouth;
}

if ($opts->{saskatoon}) {
     my $dbh = DBI->connect("DBI:mysql:database=MAST_Stoon;host=****",'****','******',{ PrintError => 1, RaiseError =>1 });
     my $sql = "select Clone_Name,Sequence from tbl_bgene";
     my $sth = $dbh->prepare($sql);
     $sth->execute();
     while (my $hash = $sth->fetchrow_hashref()) {
          # print("Name: ".$hash->{'Clone_Name'}."\n");
					print Dumper($hash);
          my $seq = new Bio::Seq(  -display_id     =>   $hash->{'Clone_Name'},
                                   -seq      =>   $hash->{'Sequence'});
          $handle->write_seq($seq);
          # print("Sequence: ".$hash->{'Sequence'}."\n");
     }
}

sub validate_options {
     my ($opts) = @_;
     if ($opts->{saskatoonfile}) {
          $opts->{saskatoon} = 1;
     }
     if (!$opts->{saskatoon}) {
         warn "You did not ask for any sequences to be extracted from MAST\n".&usage()."\n";
     }
     return $opts;
}

sub usage {
     my $returner =<<__END__;
$0
     Usage:
     --saskatoon -s <boolean>      Get the sequences from MAST_Stoon
     --saskatoonfile<filename>     Put sequences from MAST_Stoon into this file (automatically turns on -s)

./mast_fasta.pl --saskatoonfile MAST_Saskatoon 

__END__
     return $returner;   
}