use Maasha::Common;
use Maasha::Filesys;
use Maasha::Biopieces;
-use Maasha::BGB::Common;
+use Maasha::BGB::Track;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Maasha::Biopieces::put_record( $record, $out );
}
-Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Common::list_users();
+Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Track::list_users();
-@contigs = Maasha::BGB::Common::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
+@contigs = Maasha::BGB::Track::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
foreach $contig ( @contigs )
{
- @tracks = Maasha::BGB::Common::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
+ @tracks = Maasha::BGB::Track::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
foreach $track ( @tracks )
{
use strict;
use Data::Dumper;
use Maasha::Biopieces;
-use Maasha::BGB::Common;
+use Maasha::BGB::Track;
use Maasha::KISS;
Maasha::Biopieces::put_record( $record, $out );
}
-Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Common::list_users();
+Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Track::list_users();
-@contigs = Maasha::BGB::Common::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
+@contigs = Maasha::BGB::Track::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
foreach $contig ( @contigs )
{
undef %hash;
- @tracks = Maasha::BGB::Common::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
+ @tracks = Maasha::BGB::Track::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
foreach $track ( @tracks )
{
use strict;
use Data::Dumper;
use Maasha::Biopieces;
-use Maasha::BGB::Common;
+use Maasha::BGB::Track;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Maasha::Biopieces::put_record( $record, $out );
}
-Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Common::list_users();
+Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Track::list_users();
-foreach $clade ( Maasha::BGB::Common::list_clades( $options->{ 'user' } ) )
+foreach $clade ( Maasha::BGB::Track::list_clades( $options->{ 'user' } ) )
{
- foreach $genome ( Maasha::BGB::Common::list_genomes( $options->{ 'user' }, $clade ) )
+ foreach $genome ( Maasha::BGB::Track::list_genomes( $options->{ 'user' }, $clade ) )
{
- foreach $assembly ( Maasha::BGB::Common::list_assemblies( $options->{ 'user' }, $clade, $genome ) )
+ foreach $assembly ( Maasha::BGB::Track::list_assemblies( $options->{ 'user' }, $clade, $genome ) )
{
- foreach $contig ( Maasha::BGB::Common::list_contigs( $options->{ 'user' }, $clade, $genome, $assembly ) )
+ foreach $contig ( Maasha::BGB::Track::list_contigs( $options->{ 'user' }, $clade, $genome, $assembly ) )
{
- foreach $track ( Maasha::BGB::Common::list_tracks( $options->{ 'user' }, $clade, $genome, $assembly, $contig ) ) {
+ foreach $track ( Maasha::BGB::Track::list_tracks( $options->{ 'user' }, $clade, $genome, $assembly, $contig ) ) {
$dir_hash->{ $options->{ 'user' } }->{ $clade }->{ $genome }->{ $assembly }->{ $track } = 1;
}
}
use strict;
use Data::Dumper;
use Maasha::Biopieces;
-use Maasha::BGB::Common;
+use Maasha::BGB::Track;
use Maasha::KISS;
Maasha::Biopieces::put_record( $record, $out );
}
-Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Common::list_users();
+Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Track::list_users();
-@contigs = Maasha::BGB::Common::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
+@contigs = Maasha::BGB::Track::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
foreach $contig ( @contigs )
{
- @tracks = Maasha::BGB::Common::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
+ @tracks = Maasha::BGB::Track::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
foreach $track ( @tracks )
{
use Maasha::KISS;
use Maasha::Biopieces;
use Maasha::Fasta;
-use Maasha::BGB::Common;
+use Maasha::BGB::Track;
use Maasha::BGB::Wiggle;
use Maasha::Filesys;
Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
}
- $num = Maasha::BGB::Common::max_track( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
+ $num = Maasha::BGB::Track::max_track( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
$num = sprintf( "%04d", $num + 10 );
foreach $key ( keys %fh_hash )
+++ /dev/null
-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;
-}
-
-
-sub max_track
-{
- # Martin A. Hansen, December 2009.
-
- # Traverses all contigs for a given user->clade->genome->assembly and
- # returns the maximum track's prefix value eg. 20 for 20_Genbank.
-
- my ( $user,
- $clade,
- $genome,
- $assembly
- ) = @_;
-
- # Returns an integer
-
- my ( @contigs, $contig, @tracks, $max );
-
- @contigs = list_contigs( $user, $clade, $genome, $assembly );
-
- foreach $contig ( @contigs ) {
- push @tracks, list_tracks( $user, $clade, $genome, $assembly, $contig );
- }
-
- @tracks = sort @tracks;
-
- if ( scalar @tracks > 0 and $tracks[ -1 ] =~ /^(\d+)/ ) {
- $max = $1;
- } else {
- $max = 0;
- }
-
- return $max;
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-1;
if ( $line =~ /$search_term/i )
{
$entry = Maasha::KISS::kiss_entry_parse( $line );
+ $entry = Maasha::KISS::kiss2biopiece( $entry );
push @entries, $entry;
}
}
}
+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;
+}
+
+
+sub max_track
+{
+ # Martin A. Hansen, December 2009.
+
+ # Traverses all contigs for a given user->clade->genome->assembly and
+ # returns the maximum track's prefix value eg. 20 for 20_Genbank.
+
+ my ( $user,
+ $clade,
+ $genome,
+ $assembly
+ ) = @_;
+
+ # Returns an integer
+
+ my ( @contigs, $contig, @tracks, $max );
+
+ @contigs = list_contigs( $user, $clade, $genome, $assembly );
+
+ foreach $contig ( @contigs ) {
+ push @tracks, list_tracks( $user, $clade, $genome, $assembly, $contig );
+ }
+
+ @tracks = sort @tracks;
+
+ if ( scalar @tracks > 0 and $tracks[ -1 ] =~ /^(\d+)/ ) {
+ $max = $1;
+ } else {
+ $max = 0;
+ }
+
+ return $max;
+}
+
+
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
1;
projects / biopieces.git / commitdiff