renamed upload_to_bbrowser to BGB_upload

git-svn-id: http://biopieces.googlecode.com/svn/trunk@808 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/BGB_upload b/bp_bin/BGB_upload
new file mode 100755 (executable)
index 0000000..916ffa8
--- /dev/null
+++ b/bp_bin/BGB_upload
@@ -0,0 +1,182 @@
+#!/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 the KISS Genome browser.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Common;
+use Maasha::KISS;
+use Maasha::Biopieces;
+use Maasha::Fasta;
+use Maasha::Filesys;
+
+use constant {
+    SEQ_NAME => 0,
+    SEQ      => 1,
+};
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $data_dir, $user, $options, $path, $in, $out, $tmp_dir, %fh_hash, $fh_out, $record, $entry, $key, @dirs, $dir, $dst_dir, @nums, $num, $contig_dir );
+
+$data_dir = Maasha::Biopieces::biopiecesrc( "KISS_DATA_DIR" );
+$user     = Maasha::Biopieces::biopiecesrc( "KISS_USER" );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'user',       short => 'u', type => 'string', mandatory => 'no',  default => $user, allowed => undef, disallowed => undef },
+        { long => 'clade',      short => 'c', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'genome',     short => 'g', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'assembly',   short => 'a', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'track_name', short => 't', type => 'string', mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'force',      short => 'f', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+if ( $options->{ 'track_name' } )
+{
+    $options->{ 'track_name' } =~ tr/ /_/;
+
+    $path = join "/", $data_dir, "Users/", $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' };
+
+    Maasha::Common::error( qq(Path not found: "$path") ) if not -d $path;
+
+    $tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+    {
+        if ( $entry = Maasha::KISS::biopiece2kiss( $record ) )
+        {
+            $entry->{ 'S_ID' } = ( split / /, $entry->{ 'S_ID' } )[ 0 ];
+
+            if ( not exists $fh_hash{ $entry->{ 'S_ID' } } ) {
+                $fh_hash{ $entry->{ 'S_ID' } } = Maasha::Filesys::file_write_open( "$tmp_dir/$entry->{ 'S_ID' }" );
+            }
+
+            $fh_out = $fh_hash{ $entry->{ 'S_ID' } };
+
+            Maasha::KISS::kiss_entry_put( $entry, $fh_out );
+        }
+
+        Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+    }
+
+    foreach $key ( keys %fh_hash )
+    {
+        close $fh_hash{ $key };
+
+        $dst_dir = Maasha::Filesys::dir_create_if_not_exists( "$path/$key" );
+        $dst_dir = Maasha::Filesys::dir_create_if_not_exists( "$dst_dir/Tracks" );
+
+        @dirs = Maasha::Filesys::ls_dirs( $dst_dir );
+
+        foreach $dir ( @dirs )
+        {
+            $dir = ( split "/", $dir )[ -1 ];
+
+            if ( $dir =~ /^(\d+)/ ) {
+                push @nums, $1;
+            }
+        }
+
+        @nums = sort { $a <=> $b } @nums;
+
+        $num = $nums[ -1 ] || 0;
+
+        $num += 10;
+
+        $dst_dir = "$dst_dir/$num" . "_$options->{ 'track_name' }";
+
+        Maasha::Filesys::dir_create( $dst_dir );
+
+        Maasha::Filesys::file_copy( "$tmp_dir/$key", "$dst_dir/track_data.kiss" );
+
+        Maasha::KISS::kiss_sort( "$dst_dir/track_data.kiss" );
+        Maasha::KISS::kiss_index( "$dst_dir/track_data.kiss" );
+
+        unlink "$tmp_dir/$key";
+    }
+}
+else
+{
+    $path = join "/", $data_dir, "Users/", $options->{ 'user' }, $options->{ 'clade' };
+
+    Maasha::Common::error( qq(Path not found: "$path") ) if not -d $path;
+
+    $dst_dir = Maasha::Filesys::dir_create( "$path/$options->{ 'genome' }" );
+    $dst_dir = Maasha::Filesys::dir_create( "$dst_dir/$options->{ 'assembly' }" );
+
+    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+    {
+        if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
+        {
+            $entry->[ SEQ_NAME ] = ( split " ", $entry->[ SEQ_NAME ] )[ 0 ];
+
+            if ( $options->{ 'force' } ) {
+                Maasha::Filesys::dir_remove( "$dst_dir/$entry->[ SEQ_NAME ]" );
+            }
+
+            $contig_dir = Maasha::Filesys::dir_create( "$dst_dir/$entry->[ SEQ_NAME ]" );
+            $contig_dir = Maasha::Filesys::dir_create( "$contig_dir/Sequence" );
+            
+            $fh_out = Maasha::Filesys::file_write_open( "$contig_dir/sequence.txt" );
+            print $fh_out $entry->[ SEQ ];
+            close $fh_out;
+        }
+    }
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/bp_bin/upload_to_bbrowser b/bp_bin/upload_to_bbrowser
deleted file mode 100755 (executable)
index 916ffa8..0000000
--- a/bp_bin/upload_to_bbrowser
+++ /dev/null
@@ -1,182 +0,0 @@
-#!/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 the KISS Genome browser.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use warnings;
-use strict;
-use Data::Dumper;
-use Maasha::Common;
-use Maasha::KISS;
-use Maasha::Biopieces;
-use Maasha::Fasta;
-use Maasha::Filesys;
-
-use constant {
-    SEQ_NAME => 0,
-    SEQ      => 1,
-};
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my ( $data_dir, $user, $options, $path, $in, $out, $tmp_dir, %fh_hash, $fh_out, $record, $entry, $key, @dirs, $dir, $dst_dir, @nums, $num, $contig_dir );
-
-$data_dir = Maasha::Biopieces::biopiecesrc( "KISS_DATA_DIR" );
-$user     = Maasha::Biopieces::biopiecesrc( "KISS_USER" );
-
-$options = Maasha::Biopieces::parse_options(
-    [
-        { long => 'user',       short => 'u', type => 'string', mandatory => 'no',  default => $user, allowed => undef, disallowed => undef },
-        { long => 'clade',      short => 'c', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
-        { long => 'genome',     short => 'g', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
-        { long => 'assembly',   short => 'a', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
-        { long => 'track_name', short => 't', type => 'string', mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
-        { long => 'force',      short => 'f', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
-        { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
-    ]   
-);
-
-$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-if ( $options->{ 'track_name' } )
-{
-    $options->{ 'track_name' } =~ tr/ /_/;
-
-    $path = join "/", $data_dir, "Users/", $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' };
-
-    Maasha::Common::error( qq(Path not found: "$path") ) if not -d $path;
-
-    $tmp_dir = Maasha::Biopieces::get_tmpdir();
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-    {
-        if ( $entry = Maasha::KISS::biopiece2kiss( $record ) )
-        {
-            $entry->{ 'S_ID' } = ( split / /, $entry->{ 'S_ID' } )[ 0 ];
-
-            if ( not exists $fh_hash{ $entry->{ 'S_ID' } } ) {
-                $fh_hash{ $entry->{ 'S_ID' } } = Maasha::Filesys::file_write_open( "$tmp_dir/$entry->{ 'S_ID' }" );
-            }
-
-            $fh_out = $fh_hash{ $entry->{ 'S_ID' } };
-
-            Maasha::KISS::kiss_entry_put( $entry, $fh_out );
-        }
-
-        Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
-    }
-
-    foreach $key ( keys %fh_hash )
-    {
-        close $fh_hash{ $key };
-
-        $dst_dir = Maasha::Filesys::dir_create_if_not_exists( "$path/$key" );
-        $dst_dir = Maasha::Filesys::dir_create_if_not_exists( "$dst_dir/Tracks" );
-
-        @dirs = Maasha::Filesys::ls_dirs( $dst_dir );
-
-        foreach $dir ( @dirs )
-        {
-            $dir = ( split "/", $dir )[ -1 ];
-
-            if ( $dir =~ /^(\d+)/ ) {
-                push @nums, $1;
-            }
-        }
-
-        @nums = sort { $a <=> $b } @nums;
-
-        $num = $nums[ -1 ] || 0;
-
-        $num += 10;
-
-        $dst_dir = "$dst_dir/$num" . "_$options->{ 'track_name' }";
-
-        Maasha::Filesys::dir_create( $dst_dir );
-
-        Maasha::Filesys::file_copy( "$tmp_dir/$key", "$dst_dir/track_data.kiss" );
-
-        Maasha::KISS::kiss_sort( "$dst_dir/track_data.kiss" );
-        Maasha::KISS::kiss_index( "$dst_dir/track_data.kiss" );
-
-        unlink "$tmp_dir/$key";
-    }
-}
-else
-{
-    $path = join "/", $data_dir, "Users/", $options->{ 'user' }, $options->{ 'clade' };
-
-    Maasha::Common::error( qq(Path not found: "$path") ) if not -d $path;
-
-    $dst_dir = Maasha::Filesys::dir_create( "$path/$options->{ 'genome' }" );
-    $dst_dir = Maasha::Filesys::dir_create( "$dst_dir/$options->{ 'assembly' }" );
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-    {
-        if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
-        {
-            $entry->[ SEQ_NAME ] = ( split " ", $entry->[ SEQ_NAME ] )[ 0 ];
-
-            if ( $options->{ 'force' } ) {
-                Maasha::Filesys::dir_remove( "$dst_dir/$entry->[ SEQ_NAME ]" );
-            }
-
-            $contig_dir = Maasha::Filesys::dir_create( "$dst_dir/$entry->[ SEQ_NAME ]" );
-            $contig_dir = Maasha::Filesys::dir_create( "$contig_dir/Sequence" );
-            
-            $fh_out = Maasha::Filesys::file_write_open( "$contig_dir/sequence.txt" );
-            print $fh_out $entry->[ SEQ ];
-            close $fh_out;
-        }
-    }
-}
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-BEGIN
-{
-    Maasha::Biopieces::status_set();
-}
-
-
-END
-{
-    Maasha::Biopieces::status_log();
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__