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Merge pull request #3 from viklund/master
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Mafft version 6, need to poll users to see if older versions are being used
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Chris Fields committed Sep 20, 2011
2 parents 79d30c6 + b4e9463 commit 4ee6c02
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Showing 2 changed files with 138 additions and 23 deletions.
137 changes: 115 additions & 22 deletions lib/Bio/Tools/Run/Alignment/MAFFT.pm
View file
Expand Up @@ -18,13 +18,29 @@ Bio::Tools::Run::Alignment::MAFFT - run the MAFFT alignment tools
=head1 SYNOPSIS
use Bio::Tools::Run::Alignment::MAFFT;
# Build a MAFFT alignment factory
$factory = Bio::Tools::Run::Alignment::MAFFT->new(@params);
# Pass the factory a list of sequences to be aligned.
$inputfilename = 't/cysprot.fa';
# $aln is a SimpleAlign object.
$aln = $factory->align($inputfilename);
# or where @seq_array is an array of Bio::Seq objects
$seq_array_ref = \@seq_array;
$aln = $factory->align($seq_array_ref);
#There are various additional options available.
=head1 DESCRIPTION
You can get MAFFT from
L<http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft4/>.
"fftnsi" is the default in this implementation.
You can get MAFFT from L<http://mafft.cbrc.jp/alignment/software/>.
"fftnsi" is the default method for Mafft version 4 in this
implementation.
See Bio::Tools::Run::Alignment::Clustalw for a description on how to
specify parameters to the underlying alignment program. See the MAFFT
manual page for a description of the MAFFT parameters.
=head1 FEEDBACK
Expand Down Expand Up @@ -69,8 +85,8 @@ methods. Internal methods are usually preceded with a _
package Bio::Tools::Run::Alignment::MAFFT;

use vars qw($AUTOLOAD @ISA $PROGRAMNAME $PROGRAM %DEFAULTS
@MAFFT_PARAMS @MAFFT_SWITCHES @OTHER_SWITCHES %OK_FIELD
@MAFFT_ALN_METHODS
@MAFFT4_PARAMS @MAFFT4_SWITCHES @OTHER_SWITCHES %OK_FIELD
@MAFFT_ALN_METHODS @MAFFT6_PARAMS @MAFFT6_SWITCHES %OK_FIELD6
);
use strict;
use Bio::Seq;
Expand All @@ -85,14 +101,27 @@ BEGIN {
%DEFAULTS = ( 'OUTPUT' => 'fasta',
'METHOD' => 'fftnsi',
'CYCLES' => 2);
@MAFFT_PARAMS =qw( METHOD CYCLES );
@MAFFT_SWITCHES = qw( NJ ALL_POSITIVE);
@MAFFT4_PARAMS =qw( METHOD CYCLES );
@MAFFT4_SWITCHES = qw( NJ ALL_POSITIVE);

# NB: Mafft6 options are case-sensitive (eg. --lop and --LOP is different)
@MAFFT6_PARAMS = qw( weighti retree maxiterate partsize groupsize
op ep lop lep lexp LOP LEXP bl jtt tm aamatrix fmodel seed );
@MAFFT6_SWITCHES = qw( auto 6merpair globalpair localpair genafpair
fastapair fft nofft noscore memsave parttree dpparttree fastaparttree
clustalout inputorder reorder treeout nuc amino
);

@OTHER_SWITCHES = qw(QUIET ALIGN OUTPUT OUTFILE);
@MAFFT_ALN_METHODS = qw(fftnsi fftns nwnsi nwns fftnsrough nwnsrough);
#@MAFFT6_ALN_METHODS = qw(linsi ginsi einsi fftnsi fftns nwnsi nwns)
# Authorize attribute fields
foreach my $attr ( @MAFFT_SWITCHES,@MAFFT_PARAMS,@OTHER_SWITCHES ) {
foreach my $attr ( @MAFFT4_SWITCHES,@MAFFT4_PARAMS,@OTHER_SWITCHES ) {
$OK_FIELD{$attr}++;
}
foreach my $attr ( @MAFFT6_PARAMS, @MAFFT6_SWITCHES ) {
$OK_FIELD6{$attr}++
}
}

=head2 program_name
Expand Down Expand Up @@ -194,14 +223,25 @@ sub new {
}

$self->output($DEFAULTS{'OUTPUT'}) unless( $self->output );
$self->method($DEFAULTS{'METHOD'}) unless( $self->method );
if ( ! $self->_version6 ) {
$self->method($DEFAULTS{'METHOD'}) unless( $self->method );
}
return $self;
}

sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;

# NB: Mafft6 options are case-sensitive
if ( $self->_version6 ) {
if ( $OK_FIELD6{ $attr } ) {
# Don't want the attrs to clash with bioperl attributes
$self->{version6attrs}{$attr} = shift if @_;
return $self->{version6attrs}{$attr};
}
}
$attr = uc $attr;
# aliasing
$attr = 'OUTFILE' if $attr eq 'OUTFILE_NAME';
Expand Down Expand Up @@ -325,7 +365,7 @@ sub align {
=head2 _run
Title : _run
Usage : Internal function, not to be called directly
Usage : Internal function, not to be called directly
Function: makes actual system call to tcoffee program
Example :
Returns : nothing; tcoffee output is written to a
Expand Down Expand Up @@ -439,19 +479,47 @@ sub _setparams {
}
my ($attr,$value);

for $attr ( @MAFFT_SWITCHES) {
$value = $self->$attr();
next unless ($value);
my $attr_key = lc $attr; #put switches in format expected by mafft
$attr_key = ' --'.$attr_key;
$param_string .= $attr_key ;
if ( $self->_version6 ) {
for $attr ( @MAFFT6_SWITCHES) {
$value = $self->$attr();
next unless defined $value;
my $attr_key = lc $attr; #put switches in format expected by mafft
$attr_key = ' --'.$attr_key;
$param_string .= $attr_key ;
}
for $attr ( @MAFFT6_PARAMS ) {
$value = $self->$attr();
next unless (defined $value);
my $attr_key = lc $attr;
$attr_key = ' --'.$attr_key;
$param_string .= $attr_key .' '.$value;
}
if ( ! $self->no_param_checks ) {
my @incompatible = qw/auto 6merpair globalpair localpair genafpair
fastapair/;
my @set = grep { $self->$_ } @incompatible;
if ( @set > 1 ) {
$self->throw("You can't specify more than one of @set");
}
}
}
my $method = $self->method;
$self->throw("no method ") unless defined $method;
if( $method !~ /(rough|nsi)$/ &&
defined $self->cycles) {
$param_string .= " ".$self->cycles;
else {
for $attr ( @MAFFT4_SWITCHES) {
$value = $self->$attr();
next unless defined $value;
my $attr_key = lc $attr; #put switches in format expected by mafft
$attr_key = ' --'.$attr_key;
$param_string .= $attr_key ;
}
# Method is a version 4 option
my $method = $self->method;
$self->throw("no method ") unless defined $method;
if( $method !~ /(rough|nsi)$/ &&
defined $self->cycles) {
$param_string .= " ".$self->cycles;
}
}

my $outputstr = " 1>$outfile" ;

if ($self->quiet() || $self->verbose < 0) {
Expand All @@ -478,6 +546,31 @@ sub methods {
}


=head2 _version6
Title : _version6
Usage : Internal function, not to be called directly
Function: Check if the version of MAFFT is 6
Example :
Returns : Boolean
Args : None
=cut

sub _version6 {
my $self = shift;
if ( ! defined $self->{_version6} ) {
if ( $self->version =~ /^v6/ ) {
$self->{_version6} = 1;
}
else {
$self->{_version6} = '';
}
}
return $self->{_version6};
}


=head1 Bio::Tools::Run::BaseWrapper methods
=cut
Expand Down
24 changes: 23 additions & 1 deletion t/MAFFT.t
View file
Expand Up @@ -7,7 +7,7 @@ use vars qw($DEBUG);
$DEBUG = test_debug();
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 17);
test_begin(-tests => 23);
use_ok(' Bio::Tools::Run::Alignment::MAFFT');
use_ok(' Bio::AlignIO');
use_ok(' Bio::SeqIO');
Expand Down Expand Up @@ -61,4 +61,26 @@ SKIP: {
my $s1_perid = $aln->average_percentage_identity;
ok($s1_perid);
}

SKIP: {
skip("Tests require version 6 of MAFFT", 6) unless $factory->_version6;
$factory->localpair(1);
$aln = $factory->align( $inputfilename );
is $aln->num_sequences, 7;
$s1_perid = $aln->average_percentage_identity;
ok($s1_perid);

$factory->globalpair(1);
throws_ok { $aln = $factory->align( $inputfilename ) }
qr/You can't specify more than one of/,
'More than one alignment method throws';

my @extra_params = qw/ localpair 1 maxiterate 10000 /;
$factory = Bio::Tools::Run::Alignment::MAFFT->new(@params, @extra_params);
isa_ok $factory,'Bio::Tools::Run::Alignment::MAFFT';
$aln = $factory->align( $inputfilename );
is $aln->num_sequences, 7;
$s1_perid = $aln->average_percentage_identity;
ok($s1_perid);
}
}

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