/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm is in libbio-perl-run-perl 1.7.1-3.
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# BioPerl module for Bio::Tools::Run::Alignment::Pal2Nal
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Alignment::Pal2Nal - Wrapper for Pal2Nal
=head1 SYNOPSIS
use Bio::Tools::Run::Alignment::Pal2Nal;
# Make a Pal2Nal factory
$factory = Bio::Tools::Run::Alignment::Pal2Nal->new();
# Run Pal2Nal with a protein alignment file and a multi-fasta nucleotide
# file
my $aln = $factory->run($protein_alignfilename, $nucleotide_filename);
# or with Bioperl objects
$aln = $factory->run($protein_bio_simplalign, [$nucleotide_bio_seq1,
$nucleotide_bio_seq2]);
# combinations of files/ objects are possible
# $aln isa Bio::SimpleAlign of the nucleotide sequences aligned according to
# the protein alignment
=head1 DESCRIPTION
This is a wrapper for running the Pal2Nal perl script by Mikita Suyama. You
can get details here: http://coot.embl.de/pal2nal/. Pal2Nal is used for aligning
a set of nucleotide sequences based on an alignment of their translations.
You can try supplying normal pal2nal command-line arguments to new(), eg.
new() or calling arg-named methods (excluding the initial hyphen, eg.
$factory->(1) to set the - arg).
You will need to enable this Pal2Nal wrapper to find the pal2nal.pl script.
This can be done in (at least) three ways:
1. Make sure the script is in your path.
2. Define an environmental variable PAL2NALDIR which is a
directory which contains the script:
In bash:
export PAL2NALDIR=/home/username/pal2nal/
In csh/tcsh:
setenv PAL2NALDIR /home/username/pal2nal
3. Include a definition of an environmental variable PAL2NALDIR in
every script that will use this Pal2Nal wrapper module, e.g.:
BEGIN { $ENV{PAL2NALDIR} = '/home/username/pal2nal/' }
use Bio::Tools::Run::Alignment::Pal2Nal;
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::Alignment::Pal2Nal;
use strict;
use Bio::AlignIO;
use Bio::SeqIO;
use base qw(Bio::Tools::Run::Phylo::PhyloBase);
our $PROGRAM_NAME = 'pal2nal.pl';
our $PROGRAM_DIR = $ENV{'PAL2NALDIR'};
# methods for the pal2nal args we support
our @PARAMS = qw(codontable);
our @SWITCHES = qw(blockonly nogap nomismatch);
# just to be explicit, args we don't support (yet) or we handle ourselves
our @UNSUPPORTED = qw(output html h nostderr);
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns : string
Args : None
=cut
sub program_name {
return $PROGRAM_NAME;
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args : None
=cut
sub program_dir {
return $PROGRAM_DIR;
}
=head2 new
Title : new
Usage : $factory = Bio::Tools::Run::Alignment::Pal2Nal->new()
Function: creates a new Pal2Nal factory.
Returns : Bio::Tools::Run::Alignment::Pal2Nal
Args : Most options understood by pal2nal.pl can be supplied as key =>
value pairs.
These options can NOT be used with this wrapper:
-output
-html
-h
-nostderr
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->_set_from_args(\@args, -methods => [@PARAMS, @SWITCHES, 'quiet'],
-create => 1);
return $self;
}
=head2 run
Title : run
Usage : $result = $factory->run($protein_align_file, $multi_fasta_nucleotide);
-or-
$result = $factory->run($prot_align_object, [$bioseq_object1, ...]);
Function: Runs pal2nal on a protein alignment and set of nucleotide sequences.
Returns : Bio::SimpleAlign;
Args : The first argument represents a protein alignment, the second
argument a set of nucleotide sequences.
The alignment can be provided as an alignment file readable by
Bio::AlignIO, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The nucleotide sequences can be provided as a single filename of a
fasta file containing multiple nucleotide sequences, or an array ref
of filenames, each file containing one sequence. Alternatively, an
array ref of Bio::PrimarySeqI compliant objects can be supplied.
In all cases, the protein alignment sequence names must correspond to
the names of the supplied nucleotide sequences.
=cut
sub run {
my ($self, $aln, $nucs) = @_;
($aln && $nucs) || $self->throw("alignment and nucleotides must be supplied");
$aln = $self->_alignment($aln);
# gaps must be -, not .
my $fixed_aln = Bio::SimpleAlign->new();
foreach my $seq ($aln->each_seq) {
my $str = $seq->seq;
$str =~ s/\./-/g;
$fixed_aln->add_seq(Bio::LocatableSeq->new(-id => $seq->id, -seq => $str));
}
$self->_alignment($fixed_aln);
my $nucs_file;
if (-e $nucs) {
$nucs_file = $nucs;
}
elsif (ref($nucs) eq 'ARRAY') {
(my $tempfh, $nucs_file) = $self->io->tempfile('-dir' => $self->tempdir(), UNLINK => ($self->save_tempfiles ? 0 : 1));
close($tempfh);
my $sout = Bio::SeqIO->new(-file => ">".$nucs_file, -format => 'fasta');
foreach my $nuc (@{$nucs}) {
if (-e $nuc) {
my $sin = Bio::SeqIO->new(-file => $nuc);
while (my $nuc_seq = $sin->next_seq) {
$sout->write_seq($nuc_seq);
}
}
elsif (ref($nuc) && $nuc->isa('Bio::PrimarySeqI')) {
$sout->write_seq($nuc);
}
else {
$self->throw("Don't understand nucleotide argument '$nuc'");
}
}
}
else {
$self->throw("Don't understand nucleotide argument '$nucs'");
}
return $self->_run($nucs_file);
}
sub _run {
my ($self, $nucs_file) = @_;
my $exe = $self->executable || return;
my $aln_file = $self->_write_alignment;
my ($rfh, $result_file) = $self->io->tempfile('-dir' => $self->tempdir(), UNLINK => ($self->save_tempfiles ? 0 : 1));
my ($efh, $error_file) = $self->io->tempfile('-dir' => $self->tempdir(), UNLINK => ($self->save_tempfiles ? 0 : 1));
close($rfh);
undef $rfh;
close($efh);
undef $efh;
my $command = $exe.$self->_setparams($aln_file, $nucs_file, $result_file, $error_file);
$self->debug("pal2nal command = $command\n");
system($command) && $self->throw("pal2nal call ($command) failed: $! | $?");
open(my $errfh, '<', $error_file);
my $errors;
while (<$errfh>) {
$errors .= $_;
}
close($errfh);
$self->throw("pal2nal call ($command) had errors:\n$errors") if $errors;
my $ain = Bio::AlignIO->new(-file => $result_file, -format => 'fasta');
my $aln = $ain->next_aln;
$ain->close;
return $aln;
}
=head2 _setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: Creates a string of params to be used in the command string
Returns : string of params
Args : alignment and tree file names
=cut
sub _setparams {
my ($self, $aln_file, $nucs_file, $result_file, $error_file) = @_;
my $param_string = ' '.$aln_file;
$param_string .= ' '.$nucs_file;
$param_string .= $self->SUPER::_setparams(-params => \@PARAMS,
-switches => \@SWITCHES,
-dash => 1);
$param_string .= ' -output fasta';
$param_string .= " > $result_file 2> $error_file";
return $param_string;
}
1;
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