A way of printing synteny regions to screen or file from an ensembl or ensembl genomes resource

list_synteny.pl

#!/bin/env perl

use strict;
use warnings;

use Getopt::Long;
use Pod::Usage;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Utils::Scalar qw(wrap_array);
use IO::String;

my $O = options();
my $DBA = database();
my $MLSS = mlss();
my $SYNTENY = synteny();
my $FH = fh();
print_synteny();

if(!$O->{file}) {
  print ${$FH->string_ref};
}

close($FH);

exit 0;

sub options {
  my $opts = {};
  my @flags = qw(
    ensembl ensemblgenomes database=s species=s@ version=i file=s help man
  );
  GetOptions($opts, @flags) or pod2usage(1);
  
  _exit( undef, 0, 1) if $opts->{help};
	_exit( undef, 0, 2) if $opts->{man};
		
	if($opts->{ensemblgenomes} && $opts->{ensembl}) {
	  _exit( 'Can only specify -ensembl or -ensemblgenomes', 1, 2);
	}
	
	my $species = wrap_array($opts->{species});
	if(scalar(@{$species}) != 2) {
	  _exit( 'Script requires two -species attributes', 1, 2);
	}
	
	$opts->{database} = 'multi' unless $opts->{database};
	
	return $opts;
}

sub database {
  my %args;
  
  if($O->{ensemblgenomes}) {
    %args = (
      -HOST => 'mysql.ebi.ac.uk', -PORT => 4157, -USER => 'anonymous'
    );
  }
  elsif($O->{ensembl}) {
    %args = (
      -HOST => 'ensembldb.ensembl.org', -PORT => 5306, -USER => 'anonymous'
    );
  }
  else {
    _exit('Not aware of which server I should connect to. Specify -ensembl or -ensemblgenomes', 2, 1);
  }
  
  if($O->{version}) {
    $args{-DB_VERSION} = $O->{version};
  }
  
  Bio::EnsEMBL::Registry->load_registry_from_db(%args);
  my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($O->{database}, 'compara');
  
  if(! defined $dba) {
    _exit($O->{database}.' did not result in a valid DB. Try again specifying a different -database parameter. Also check your -version switch and API version', 2, 1);
  }
  
  return $dba;
}

sub mlss {
  my $species = $O->{species};
  my $gdba = $DBA->get_GenomeDBAdaptor();
  my $mlssa = $DBA->get_MethodLinkSpeciesSetAdaptor();
  my @gdbs = map { $gdba->fetch_by_registry_name($_) } @{$species};
  my $mlss = $mlssa->fetch_by_method_link_type_GenomeDBs('SYNTENY', \@gdbs);
  return $mlss;
}

sub synteny {
  my $sra = $DBA->get_SyntenyRegionAdaptor();
  my $regions = $sra->fetch_all_by_MethodLinkSpeciesSet($MLSS);
  return $regions;
}

sub fh {
  if($O->{file}) {
    return IO::File->new($O->{file}, 'w');
  }
  return IO::String->new();
}

sub print_synteny {
  my ($source_gdb, $target_gdb) = @{$MLSS->species_set()->genome_dbs()};
  my $sname = $source_gdb->name();
  my $tname = $target_gdb->name();
  
  print $FH sprintf(
    'track name=synteny_%1$s description="%1$s %2$s synteny projections"', 
    $sname, $tname);
  print $FH "\n";
  
  foreach my $s (@{$SYNTENY}) {
    my $regions = $s->get_all_DnaFragRegions();
    my ($source) = grep { $_->genome_db()->dbID() eq $source_gdb->dbID() } @{$regions};
    my ($target) = grep { $_->genome_db()->dbID() eq $target_gdb->dbID() } @{$regions};
    
    my $create_elements = sub {
      my ($frag) = @_;
      return (
        $frag->dnafrag()->name(), #name of region
        $frag->dnafrag()->length(), #length of region e.g. chr1 in human
        $frag->dnafrag_start(), #start of alignment
        $frag->dnafrag_end() #end of alignment
      );
    };
    
    my @data = (
      $source->length(),
      0, #misMatches
      0, #repMatches 
      0, #nCount
      0, #qNumInsert
      0, #qBaseInsert
      0, #tNumInsert
      0, #tBaseInsert
      ( $source->dnafrag_strand() ) ? '+' : '-', #strand,
      $create_elements->($source), #query info
      $create_elements->($target), #target info
      1, # number of blocks
      $source->length(), #block sizes
      $source->dnafrag_start(), #query start blocks
      $target->dnafrag_start() #target start blocks
    );
    
    print $FH join(q{ }, @data), "\n";
  }
  
  return;
}

sub _exit {
  my ($msg, $status, $verbose) = @_;
  print STDERR $msg, "\n" if defined $msg;
  pod2usage( -exitstatus => $status, -verbose => $verbose );
}

__END__
=pod

=head1 NAME

list_synteny.pl

=head1 SYNOPSIS 

	./list_synteny.pl -species human -species mouse -ensembl -database multi [see opts] [ --help | --man ]
	
=head1 DESCRIPTION

Returns a PSL to screen or to a specified file location

=head1 OPTIONS

=over 8

=item B<--species>

Accepts 2 invocations to specify the species to look for synteny between

=item B<--ensembl>

Specify to connect to the public ensembl database

=item B<--ensemblgenomes>

Specify to connect to the public ensembl genomes database

=item B<--database>

Specify the name of the database to connect to. If going to ensembl
use multi otherwise if connecting to ensembl genomes use one like
plants, metazoa, protists, bacteria or fungi (not all DBs have synteny 
projections though).

=item B<--version>

Optional integer which can be used to force the databases we load. Useful if
your API does not match the DB you are connecting to.

=item B<--file>

Location of the file to write to. If not specified will write to STDOUT

=back

=head1 VERSION

1

=head1 LICENSE

 Copyright (c) 1999-2011 The European Bioinformatics Institute and
 Genome Research Limited.  All rights reserved.

 This software is distributed under a modified Apache license.
 For license details, please see

   http://www.ensembl.org/info/about/code_licence.html

=cut

Unfortunately, it doesn't work for me. I get an error 'Not an ARRAY reference at list_synteny.pl line 105.'. When I change the array reference to hash (changing @ to %), I get further errors 'Can't locate object method "name" via package "adaptor" (perhaps you forgot to load "adaptor"'

I'm also aware that there are getsynteny.pl script under this link https://github.com/Ensembl/ensembl-compara/tree/release/107/scripts/synteny, but I'm struggling on how to use it correctly as well.

Do you mind helping me out with those? I really need this information for my undergrad thesis.

I've just updated this gist. The error was because I believe lots of years ago ->species_set() would return an array, where as now it returns an object. Changing line 105's dereferencing to @{$MLSS->species_set()->genome_dbs()} has fixed the issue. Verified by trying to extract human/mouse synteny.

Thank you so much for doing this!!

Last question: What version of perl are you using? I still get an issue in the line 109 saying "Can't use an undefined value as a symbol reference at list_synteny.pl"

Mine is following: This is perl 5, version 32, subversion 0 (v5.32.0) built for darwin-2level

I'm running This is perl 5, version 34, subversion 1 (v5.34.1) built for darwin-2level and do not see any issue on my side sorry. The command I ran was: perl list_synteny.pl -species human -species mouse -ensembl.

With respect to the error, this happens when a filehandle becomes undefined. You can see from the code that we initialise $FH on line 16 before trying to print to it in print_synteny. Are you working with a clean version of the script or a modified version? This certainly should work. Also try updating IO::String and IO::File modules in-case there is an issue with them

Okay, so I had to specify use IO::File and get rid of line 23 close($FH);, and now it works!! Thanks a lot, Andrew!