added upload_to_KISS

git-svn-id: http://biopieces.googlecode.com/svn/trunk@703 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/upload_to_KISS b/bp_bin/upload_to_KISS
new file mode 100755 (executable)
index 0000000..f577d12
--- /dev/null
+++ b/bp_bin/upload_to_KISS
@@ -0,0 +1,201 @@
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Write Biopiece records to a KISS MySQL database.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Common;
+use Maasha::SQL;
+use Maasha::KISS::IO;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $user, $password, $dbh, $in, $out, $tmp_dir, $tmp_file, $fh_out, $record, $entry );
+
+$user     = Maasha::Biopieces::biopiecesrc( "MYSQL_USER" );
+$password = Maasha::Biopieces::biopiecesrc( "MYSQL_PASSWORD" );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'user',             short => 'u', type => 'string', mandatory => 'no',  default => $user,     allowed => undef, disallowed => undef },
+        { long => 'password',         short => 'p', type => 'string', mandatory => 'no',  default => $password, allowed => undef, disallowed => undef },
+        { long => 'database',         short => 'd', type => 'string', mandatory => 'yes', default => undef,     allowed => undef, disallowed => undef },
+        { long => 'table',            short => 't', type => 'string', mandatory => 'yes', default => undef,     allowed => undef, disallowed => undef },
+        { long => 'table_replace',    short => 'T', type => 'flag',   mandatory => 'no' , default => undef,     allowed => undef, disallowed => undef },
+        { long => 'table_append',     short => 'A', type => 'flag',   mandatory => 'no' , default => undef,     allowed => undef, disallowed => undef },
+        { long => 'no_stream',        short => 'x', type => 'flag',   mandatory => 'no',  default => undef,     allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$tmp_dir  = Maasha::Biopieces::get_tmpdir();
+$tmp_file = "$tmp_dir/upload_to_KISS.kiss";
+
+$dbh = Maasha::SQL::connect( $options->{ 'database' }, $options->{ 'user' }, $options->{ 'password' } );
+
+if ( Maasha::SQL::table_exists( $dbh, $options->{ 'table' } ) )
+{
+    if ( not $options->{ 'table_replace' } and not $options->{ 'table_append' } ) {
+        Maasha::Common::error( qq(Table "$options->{ 'table' }" exists. Use --table_replace or --table_append) )
+    }
+
+    if ( $options->{ 'table_replace' } ) {
+        Maasha::SQL::delete_table( $dbh, $options->{ 'table' } ) if Maasha::SQL::table_exists( $dbh, $options->{ 'table' } );
+    }
+
+    if ( $options->{ 'sql' } ) {
+        Maasha::SQL::request( $dbh, $options->{ 'sql' } );
+    } elsif ( not $options->{ 'table_append' } ) {
+        create_table( $dbh, $options->{ 'table' }, $options->{ 'verbose' } );
+    }
+}
+else
+{
+    create_table( $dbh, $options->{ 'table' }, $options->{ 'verbose' } );
+}
+
+$fh_out = Maasha::Filesys::file_write_open( $tmp_file );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $entry = Maasha::KISS::IO::biopiece2kiss( $record ) )
+    {
+        map { $entry->{ $_ } = '\N' if $entry->{ $_ } eq '.' } keys %{ $entry };
+
+        Maasha::KISS::IO::kiss_entry_put( $entry, $fh_out );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+close $fh_out;
+
+bulk_load_file( $dbh, $tmp_file, $options->{ 'table' }, $options->{ 'verbose' } );
+
+Maasha::SQL::disconnect( $dbh );
+
+unlink $tmp_file;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub bulk_load_file
+{
+    # Martin A. Hansen, October 2009
+    #
+    # Bulk load a tab separated file to MySQL while
+    # converting . to NULL.
+    
+    my ( $dbh,   # Database handle
+         $file,   # File to load
+         $table,   # Table name
+         $verbose,   # Verbose flag
+       ) = @_;
+
+    # Returns nothing.
+
+    my ( $sql );
+
+    #LOAD DATA INFILE....(col1, @dummy) SET col2 = IF(@dummy = '.', NULL, @dummy)
+
+    $sql = qq(LOAD DATA LOCAL INFILE "$file" INTO TABLE $table);
+
+    print STDERR "$sql\n" if $verbose;
+
+    Maasha::SQL::request( $dbh, $sql );
+}
+
+
+sub create_table
+{
+    # Martin A. Hansen, July 2009
+
+    # Create a new MySQL table.
+
+    my ( $dbh,            # Database handle
+         $table,          # Table name
+         $verbose,        # Verbose switch
+       ) = @_;
+
+    # Returns nothing.
+
+    my ( @fields, $field_str, $sql );
+
+    @fields = (
+        "S_ID VARCHAR(256),   INDEX S_ID_index        (S_ID)",
+        "S_BEG INT,           INDEX S_BEG_index       (S_BEG)",
+        "S_LEN INT,           INDEX S_LEN_index       (S_LEN)",
+        "Q_ID VARCHAR(256),   INDEX Q_ID_index        (Q_ID)",
+        "SCORE FLOAT,         INDEX SCORE_index       (SCORE)",
+        "STRAND CHAR(1),      INDEX STRAND_index      (STRAND)",
+        "HITS INT,            INDEX HITS_index        (HITS)",
+        "ALIGN VARCHAR(256)",
+        "BLOCK_COUNT TINYINT, INDEX BLOCK_COUNT_index (BLOCK_COUNT)",
+        "BLOCK_BEGS VARCHAR(1024)",
+        "BLOCK_LENS VARCHAR(1024)",
+    );
+
+    $field_str = join( ", ", @fields ); 
+
+    $sql = "CREATE TABLE $table ($field_str)";
+
+    print STDERR "$sql\n" if $verbose;
+
+    Maasha::SQL::request( $dbh, $sql );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::SQL::disconnect( $dbh ) if $dbh;
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__