Skip to content

Update Phyml.pm #49

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 5 commits into
base: master
Choose a base branch
from
Open

Update Phyml.pm #49

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
35233d0
Update Phyml.pm
qifei9 Mar 20, 2017
2734909
Update Phyml.pm
qifei9 Mar 21, 2017
88359c1
Merge branch 'master' of https://github.com/bioperl/bioperl-run
qifei9 Jun 6, 2017
9ee51b7
Merge remote-tracking branch 'upstream/master'
qifei9 Nov 5, 2017
38367b2
fix to get version of phyml
qifei9 Apr 25, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
75 changes: 42 additions & 33 deletions lib/Bio/Tools/Run/Phylo/Phyml.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -249,26 +249,26 @@ sub new {
%args
);

$self->data_type($data_type) if $data_type;
$self->data_format($data_format) if $data_format;
$self->dataset_count($dataset_count) if $dataset_count;
$self->model($model) if $model;
$self->freq($freq) if $freq;
$self->kappa($kappa) if $kappa;
$self->invar($invar) if $invar;
$self->category_number($category_number) if $category_number;
$self->alpha($alpha) if $alpha;
$self->tree($tree) if $tree;
$self->opt_topology($opt_topology) if $opt_topology;
$self->opt_lengths($opt_lengths) if $opt_lengths;
$self->opt($opt) if $opt;
$self->search($search) if $search;
$self->rand_start($rand_start) if $rand_start;
$self->rand_starts($rand_starts) if $rand_starts;
$self->rand_seed($rand_seed) if $rand_seed;
$self->no_memory_check($no_memory_check) if $no_memory_check;
$self->bootstrap($bootstrap) if $bootstrap;
$self->program_name($program_name) if $program_name;
$self->data_type($data_type) if defined $data_type;
$self->data_format($data_format) if defined $data_format;
$self->dataset_count($dataset_count) if defined $dataset_count;
$self->model($model) if defined $model;
$self->freq($freq) if defined $freq;
$self->kappa($kappa) if defined $kappa;
$self->invar($invar) if defined $invar;
$self->category_number($category_number) if defined $category_number;
$self->alpha($alpha) if defined $alpha;
$self->tree($tree) if defined $tree;
$self->opt_topology($opt_topology) if defined $opt_topology;
$self->opt_lengths($opt_lengths) if defined $opt_lengths;
$self->opt($opt) if defined $opt;
$self->search($search) if defined $search;
$self->rand_start($rand_start) if defined $rand_start;
$self->rand_starts($rand_starts) if defined $rand_starts;
$self->rand_seed($rand_seed) if defined $rand_seed;
$self->no_memory_check($no_memory_check) if defined $no_memory_check;
$self->bootstrap($bootstrap) if defined $bootstrap;
$self->program_name($program_name) if defined $program_name;

return $self;
}
Expand Down Expand Up @@ -333,10 +333,10 @@ sub version {

return $self->{'_version'} if defined $self->{'_version'};
my $exe = $self->executable || return;
my $string = substr `$exe -h`, 0, 40;
my $string = substr `$exe -h`, 0, 80;
my ($version) = $string =~ /PhyML v([\d+\.]+)/;
if ( !$version ) {
$string =~ /PhyML\s+(\d{8})/;
$string =~ /PhyML\s+\d+\.\d+\.(\d{8})/;

# 3 was released August 2008
$version = 3 if ( $1 && $1 >= 20080801 );
Expand Down Expand Up @@ -731,7 +731,7 @@ These methods can be used with PhyML v3* only.
Title : freq
Usage : $phyml->freq(e); $phyml->freq("0.2, 0.6, 0.6, 0.2");
Function: Sets nucleotide frequences or asks residue to be estimated
according to two models: e or d
according to two models: e or m
Returns : set value,
Args : None to get, string to set.

Expand All @@ -747,7 +747,7 @@ sub freq {
die "Invalid value [$value]"
unless $value =~ /^[\d\. ]$/
or $value eq 'e'
or $value eq 'd';
or $value eq 'm';
$self->{_freq} = $value;
}
return $self->{_freq};
Expand Down Expand Up @@ -821,7 +821,7 @@ sub rand_start {
$self->{_rand_start} = 0;
}
}
return $self->{_rand_start};
return $self->{_rand_start} || 0;
}

=head2 rand_starts
Expand All @@ -845,7 +845,11 @@ sub rand_starts {
unless $value =~ /^[-+]?\d+$/;
$self->{_rand_starts} = $value;
}
return $self->{_rand_starts} || 1;
if ($self->{_rand_starts} != 1){
return $self->{_rand_starts};
}else{
return 1;
}
}

=head2 rand_seed
Expand Down Expand Up @@ -903,7 +907,7 @@ sub no_memory_check {

Title : bootstrap
Usage : $factory->bootstrap(100);
Function: Set number of bootstraps
Function: Set number of bootstraps or type of fast likehood-based method
Returns :
Args : None to get, integer to set.

Expand All @@ -914,7 +918,9 @@ sub bootstrap {
$self->throw("Not a valid parameter [bootstrap] prior to PhyML v3")
if $self->version < 3;
if ( defined $value ) {
die "Invalid number [$value]" unless $value =~ /^\d+$/;
die "Invalid number [$value]"
unless $value =~ /^\d+$/
or $value =~ /^-[1, 2, 4, 5]$/;
$self->{_bootstrap} = $value;
}
return $self->{_bootstrap};
Expand Down Expand Up @@ -1023,13 +1029,13 @@ sub _setparams {
$param_string .= ' -q ' if $self->data_format eq 's';
$param_string .= ' -n ' . $self->dataset_count
if $self->dataset_count > 1;
$param_string .= ' -b ' . $self->bootstrap if $self->bootstrap;
$param_string .= ' -b ' . $self->bootstrap if defined $self->bootstrap;

# $param_string .= ' 0'; # no bootstrap sets
$param_string .= ' -m ' . $self->model;
$param_string .= ' -f ' . $self->freq if $self->freq;

if ( $self->data_type eq 'dna' ) {
if ( $self->data_type eq 'nt' ) {
$param_string .= ' -t ' . $self->kappa;
}

Expand Down Expand Up @@ -1082,7 +1088,7 @@ sub _setparams {
Function: Internal (not to be used directly)

Writes the alignment into the tmp directory
in PHYLIP interlieved format
in PHYLIP format

Returns : filename
Args : Bio::Align::AlignI
Expand All @@ -1093,11 +1099,14 @@ sub _write_phylip_align_file {
my ( $self, $align ) = @_;

my $tempfile = File::Spec->catfile( $self->tempdir, "aln$$.phylip" );
$self->data_format('i');
my $interleaved = 1;
if($self->data_format eq 's'){
$interleaved = 0;
}
my $out = Bio::AlignIO->new(
-file => ">$tempfile",
-format => 'phylip',
-interleaved => 1,
-interleaved => $interleaved,
-longid => 1
);
$out->write_aln($align);
Expand Down