added BGB_list

git-svn-id: http://biopieces.googlecode.com/svn/trunk@806 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/BGB_list b/bp_bin/BGB_list
new file mode 100755 (executable)
index 0000000..1cc1c0b
--- /dev/null
+++ b/bp_bin/BGB_list
@@ -0,0 +1,120 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# List all tracks availible in a local installation of the Biopieces Genome Browser.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::BGB::Common;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $user, $options, $in, $out, $record, $dir_hash, $clade, $genome, $assembly, $contig, $track );
+
+$user    = Maasha::Biopieces::biopiecesrc( "BPB_USER" );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'user', short => 'u', type => 'string', mandatory => 'yes', default => $user, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Common::list_users();
+
+foreach $clade ( Maasha::BGB::Common::list_clades( $options->{ 'user' } ) )
+{
+    foreach $genome ( Maasha::BGB::Common::list_genomes( $options->{ 'user' }, $clade ) )
+    {
+        foreach $assembly ( Maasha::BGB::Common::list_assemblies( $options->{ 'user' }, $clade, $genome ) )
+        {
+            foreach $contig ( Maasha::BGB::Common::list_contigs( $options->{ 'user' }, $clade, $genome, $assembly ) )
+            {
+                foreach $track ( Maasha::BGB::Common::list_tracks( $options->{ 'user' }, $clade, $genome, $assembly, $contig ) ) {
+                    $dir_hash->{ $options->{ 'user' } }->{ $clade }->{ $genome }->{ $assembly }->{ $track } = 1;
+                }
+            }
+        }
+    }
+}
+
+foreach $clade ( keys %{ $dir_hash->{ $options->{ 'user' } } } )
+{
+    foreach $genome ( keys %{ $dir_hash->{ $options->{ 'user' } }->{ $clade } } )
+    {
+        foreach $assembly ( keys %{ $dir_hash->{ $options->{ 'user' } }->{ $clade }->{ $genome } } )
+        {
+            foreach $track ( keys %{ $dir_hash->{ $options->{ 'user' } }->{ $clade }->{ $genome }->{ $assembly } } )
+            {
+                $record = {
+                    USER     => $options->{ 'user' },
+                    CLADE    => $clade,
+                    GENOME   => $genome,
+                    ASSEMBLY => $assembly,
+                    TRACK    => $track,
+                };
+
+                Maasha::Biopieces::put_record( $record, $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_conf/bashrc b/bp_conf/bashrc
index 0a113aee592c30a3c4b1a7f8502d2a09e4f9dadc..62e6d221cfdf7f73899be35436fc685d2348235d 100644 (file)
--- a/bp_conf/bashrc
+++ b/bp_conf/bashrc
@@ -16,6 +16,10 @@ export BP_C="$BP_DIR/code_c"                # Direcotory with C code.
 export BP_PYTHON="$BP_DIR/code_python"      # Direcotory with Pyton code.
 export BP_RUBY="$BP_DIR/code_ruby"          # Direcotory with Ruby code.
 
+### This is the directory with the document root fro the Biopieces Genome Browser:
+
+export BP_WWW="$BP_DIR/www"                 # Direcotory with Biopieces Genome Browser.
+
 ### Here we add the biopiece variable to the existing PATH.
 
 export PATH="$PATH:$BP_BIN"

diff --git a/code_perl/Maasha/BGB/Common.pm b/code_perl/Maasha/BGB/Common.pm
new file mode 100644 (file)
index 0000000..aa5842c
--- /dev/null
+++ b/code_perl/Maasha/BGB/Common.pm
@@ -0,0 +1,355 @@
+package Maasha::BGB::Common;
+
+# Copyright (C) 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+# Common routines for manipulating the Biopieces Genome Browser.
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Common;
+use Maasha::Filesys;
+use Maasha::Biopieces;
+
+use vars qw( @ISA @EXPORT );
+
+@ISA = qw( Exporter );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub list_user_dir
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all users directories in the ~/Data/Users
+    # directory with full path.
+
+    # Returns a list.
+
+    my ( @dirs, @users );
+
+    Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+
+    @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users" );
+
+    @users = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+    return wantarray ? @users : \@users;
+}
+
+
+sub list_users
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all users in ~/Data/Users
+
+    # Returns a list.
+    
+    my ( @dirs, $dir, @users );
+
+    @dirs = list_user_dir();
+
+    foreach $dir ( @dirs ) {
+        push @users, ( split "/", $dir )[ -1 ];
+    }
+
+    return wantarray ? @users : \@users;
+}
+
+
+sub list_clade_dir
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all clades for a given user in ~/Data/Users
+
+    my ( $user,   # user for which to return clades
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @dirs, @clades );
+
+    Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+    Maasha::Common::error( 'no user specified' ) if not $user;
+
+    @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user" );
+
+    @clades = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+    return wantarray ? @clades : \@clades;
+}
+
+
+sub list_clades
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all clades for a given user in ~/Data/Users
+
+    my ( $user,   # user for which to return clades
+       ) = @_;
+
+    # Returns a list.
+    
+    my ( @dirs, $dir, @clades );
+
+    @dirs = list_clade_dir( $user );
+
+    foreach $dir ( @dirs ) {
+        push @clades, ( split "/", $dir )[ -1 ];
+    }
+
+    return wantarray ? @clades : \@clades;
+}
+
+
+sub list_genome_dir
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all genomes for a given user and clade in ~/Data/Users
+
+    my ( $user,    # user for which to return genomes
+         $clade,   # clade for which to return genomes
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @dirs, @genomes );
+
+    Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+    Maasha::Common::error( 'no user specified' ) if not $user;
+    Maasha::Common::error( 'no clade specified' ) if not $clade;
+
+    @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade" );
+
+    @genomes = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+    return wantarray ? @genomes : \@genomes;
+}
+
+
+sub list_genomes
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all genomes for a given user and clade in ~/Data/Users
+
+    my ( $user,    # user for which to return genomes
+         $clade,   # clade for which to return genomes
+       ) = @_;
+
+    # Returns a list.
+    
+    my ( @dirs, $dir, @genomes );
+
+    @dirs = list_genome_dir( $user, $clade );
+
+    foreach $dir ( @dirs ) {
+        push @genomes, ( split "/", $dir )[ -1 ];
+    }
+
+    return wantarray ? @genomes : \@genomes;
+}
+
+
+sub list_assembly_dir
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all assemblies for a given user and clade and genome in ~/Data/Users
+
+    my ( $user,     # user for which to return assemblies
+         $clade,    # clade for which to return assemblies
+         $genome,   # genome for which to return assemblies
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @dirs, @assemblies );
+
+    Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+    Maasha::Common::error( 'no user specified' ) if not $user;
+    Maasha::Common::error( 'no clade specified' ) if not $clade;
+    Maasha::Common::error( 'no genome specified' ) if not $genome;
+
+    @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome" );
+
+    @assemblies = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+    return wantarray ? @assemblies : \@assemblies;
+}
+
+
+sub list_assemblies
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all assemblies for a given user and clade and genome in ~/Data/Users
+
+    my ( $user,     # user for which to return assemblies
+         $clade,    # clade for which to return assemblies
+         $genome,   # genome for which to return assemblies
+       ) = @_;
+
+    # Returns a list.
+    
+    my ( @dirs, $dir, @assemblies );
+
+    @dirs = list_assembly_dir( $user, $clade, $genome );
+
+    foreach $dir ( @dirs ) {
+        push @assemblies, ( split "/", $dir )[ -1 ];
+    }
+
+    return wantarray ? @assemblies : \@assemblies;
+}
+
+
+sub list_contig_dir
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all assemblies for a given user->clade->genome->assembly in ~/Data/Users
+
+    my ( $user,       # user for which to return contigs
+         $clade,      # clade for which to return contigs
+         $genome,     # genome for which to return contigs
+         $assembly,   # assembly for which to return contigs
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @dirs, @contigs );
+
+    Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+    Maasha::Common::error( 'no user specified' ) if not $user;
+    Maasha::Common::error( 'no clade specified' ) if not $clade;
+    Maasha::Common::error( 'no genome specified' ) if not $genome;
+    Maasha::Common::error( 'no assembly specified' ) if not $assembly;
+
+    @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome/$assembly" );
+
+    @contigs = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+    return wantarray ? @contigs : \@contigs;
+}
+
+
+sub list_contigs
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all contigs for a given user->clade->genome->assembly in ~/Data/Users
+
+    my ( $user,       # user for which to return contigs
+         $clade,      # clade for which to return contigs
+         $genome,     # genome for which to return contigs
+         $assembly,   # assembly for which to return contigs
+       ) = @_;
+
+    # Returns a list.
+    
+    my ( @dirs, $dir, @contigs );
+
+    @dirs = list_contig_dir( $user, $clade, $genome, $assembly );
+
+    foreach $dir ( @dirs ) {
+        push @contigs, ( split "/", $dir )[ -1 ];
+    }
+
+    return wantarray ? @contigs : \@contigs;
+}
+
+
+sub list_track_dir
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all tracks for a given user->clade->genome->assembly->contig in ~/Data/Users
+
+    my ( $user,       # user for which to return tracks
+         $clade,      # clade for which to return tracks
+         $genome,     # genome for which to return tracks
+         $assembly,   # assembly for which to return tracks
+         $contig,     # contig for which to return tracks
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @dirs, @tracks );
+
+    Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+    Maasha::Common::error( 'no user specified' ) if not $user;
+    Maasha::Common::error( 'no clade specified' ) if not $clade;
+    Maasha::Common::error( 'no genome specified' ) if not $genome;
+    Maasha::Common::error( 'no assembly specified' ) if not $assembly;
+    Maasha::Common::error( 'no contig specified' ) if not $contig;
+
+    if ( -d "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome/$assembly/$contig/Tracks" ) {
+        @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome/$assembly/$contig/Tracks" );
+    }
+
+    @tracks = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+    return wantarray ? @tracks : \@tracks;
+}
+
+
+sub list_tracks
+{
+    # Martin A. Hansen, December 2009.
+
+    # List all tracks for a given user->clade->genome->assembly->contig in ~/Data/Users
+
+    my ( $user,       # user for which to return tracks
+         $clade,      # clade for which to return tracks
+         $genome,     # genome for which to return tracks
+         $assembly,   # assembly for which to return tracks
+         $contig,     # contig for which to return tracks
+       ) = @_;
+
+    # Returns a list.
+    
+    my ( @dirs, $dir, @tracks );
+
+    @dirs = list_track_dir( $user, $clade, $genome, $assembly, $contig );
+
+    foreach $dir ( @dirs ) {
+        push @tracks, ( split "/", $dir )[ -1 ];
+    }
+
+    return wantarray ? @tracks : \@tracks;
+}
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+1;