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# BioPerl module for Bio::Tools::Run::Alignment::Probcons
#
# Cared for by Albert Vilella
#
#
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
HideShow 113 lines of Pod
=head1 NAME
Bio::Tools::Run::Alignment::Probcons - Object for the calculation of an
iterative multiple sequence alignment from a set of unaligned
sequences or alignments using the Probcons program
=head1 SYNOPSIS
  # Build a muscle alignment factory
  $factory = new Bio::Tools::Run::Alignment::Probcons (@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);
  # Or one can pass the factory a pair of (sub)alignments
  #to be aligned against each other, e.g.:
  #There are various additional options and input formats available.
  #See the DESCRIPTION section that follows for additional details.
  #To run probcons with training, try something like:
  #First round to generate train.params
  $factory = new Bio::Tools::Run::Alignment::Probcons
      (
       'iterative-refinement'  => '1000',
       'consistency'   => '5',
       'pre-training' => '20',
       'emissions' => '',
       'verbose' => '',
       'train'   => "$dir/$subdir/$outdir/train.params",
      );
  $factory->outfile_name("$dir/$subdir/$outdir/train.params");
  #Second round to use train.params to get a high qual alignment
  $seq_array_ref = \@seq_array;
  $aln = $factory->align($seq_array_ref);
  $aln = '';
  $factory = '';
  $factory = new Bio::Tools::Run::Alignment::Probcons
      (
       'iterative-refinement'  => '1000',
       'consistency'   => '5',
       'pre-training' => '20',
       'verbose' => '',
       'paramfile'   => "$dir/$subdir/$outdir/train.params",
      );
  $factory->outfile_name("$dir/$subdir/$outdir/outfile.afa");
  $aln = $factory->align($seq_array_ref);
=head1 DESCRIPTION
Probcons is a Probabilistic Consistency-based Multiple Alignment of
Amino Acid Sequences. You can get it and see information about it at this URL
http://probcons.stanford.edu/
=head2 Helping the module find your executable 
You will need to enable Probcons to find the probcons program. This can be
done in (at least) three ways:
  1. Make sure the probcons executable is in your path (i.e. 
     'which probcons' returns a valid program
  2. define an environmental variable PROBCONSDIR which points to a 
     directory containing the 'probcons' app:
   In bash 
        export PROBCONSDIR=/home/progs/probcons   or
   In csh/tcsh
        setenv PROBCONSDIR /home/progs/probcons
  3. include a definition of an environmental variable PROBCONSDIR 
      in every script that will
     BEGIN {$ENV{PROBCONSDIR} = '/home/progs/probcons'; }
     use Bio::Tools::Run::Alignment::Probcons;
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the web:
 http://bugzilla.open-bio.org/
=head1 AUTHOR -  Jason Stajich
Email jason-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::Alignment::Probcons;
use vars qw($AUTOLOAD @ISA $PROGRAMNAME $PROGRAM %DEFAULTS
            @PROBCONS_PARAMS @PROBCONS_SWITCHES @OTHER_SWITCHES 
            %OK_FIELD
            );
use strict;
use Bio::Seq;
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Factory::ApplicationFactoryI;
use  Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase 
          Bio::Factory::ApplicationFactoryI);
BEGIN {
    %DEFAULTS = ( 'AFORMAT' => 'fasta' );
    @PROBCONS_PARAMS = qw (CONSISTENCY ITERATIVE-REFINEMENT 
                           PRE-TRAINING ANNOT TRAIN PARAMFILE MATRIXFILE
                           CLUSTALW PAIRS VITERBI VERBOSE EMISSIONS); 
                           #FIXME: Last line are switches, dunno how to set them, 
                           #gave as params
    @PROBCONS_SWITCHES = qw();
    @OTHER_SWITCHES = qw();
# Authorize attribute fields
    foreach my $attr ( @PROBCONS_PARAMS, @OTHER_SWITCHES ) {
        $OK_FIELD{$attr}++; }
}
HideShow 10 lines of Pod
=head2 program_name
 Title   : program_name
 Usage   : $factory->program_name()
 Function: holds the program name
 Returns:  string
 Args    : None
=cut
sub program_name {
        return 'probcons';
}
HideShow 10 lines of Pod
=head2 program_dir
 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtiained from ENV variable.
 Returns:  string
 Args    :
=cut
sub program_dir {
        return Bio::Root::IO->catfile($ENV{PROBCONSDIR}) if $ENV{PROBCONSDIR};
}
HideShow 11 lines of Pod
=head2 new
 Title   : new
 Usage   : my $probcons = Bio::Tools::Run::Alignment::Probcons->new();
 Function: Constructor
 Returns : Bio::Tools::Run::Alignment::Probcons
 Args    : -outfile_name => $outname
=cut
sub new{
    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($on) = $self->SUPER::_rearrange([qw(OUTFILE_NAME)], @args);
    $self->outfile_name($on || '');
    my ($attr, $value);    
    $self->aformat($DEFAULTS{'AFORMAT'});
     
    while ( @args)  {
        $attr =   shift @args;
        $value =  shift @args;
        next if( $attr =~ /^-/); # don't want named parameters
        $self->$attr($value);
    if ($attr =~ /verbose/i) {
        $self->{verbose_set} = 1;
    }
    }
    return $self;
}
sub AUTOLOAD {
    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    # aliasing
    $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
    $self->{$attr} = shift if @_;
    return $self->{$attr};
}
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=head2 error_string
 Title   : error_string
 Usage   : $obj->error_string($newval)
 Function: Where the output from the last analysus run is stored.
 Returns : value of error_string
 Args    : newvalue (optional)
=cut
sub error_string{
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'error_string'} = $value;
    }
    return $self->{'error_string'};
}
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=head2  version
 Title   : version
 Usage   : exit if $prog->version() < 1.8
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none
=cut
sub version {
    my ($self) = @_;
    my $exe;
    return undef unless $exe = $self->executable;
    my $string = `$exe 2>&1` ;
    #PROBCONS version 1.09 - align multiple protein sequences and print to standard output
    $string =~ /PROBCONS\s+version\s+(\d+\.\d+)/m;
    return $1 || undef;
}
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=head2 run
 Title   : run
 Usage   : my $output = $application->run(\@seqs);
 Function: Generic run of an application
 Returns : Bio::SimpleAlign object
 Args    : Arrayref of Bio::PrimarySeqI objects or
           a filename to run on
=cut
sub run {
    my $self = shift;
    return $self->align(shift);
}
HideShow 24 lines of Pod
=head2  align
 Title   : align
 Usage   :
        $inputfilename = 't/data/cysprot.fa';
        $aln = $factory->align($inputfilename);
or
        $seq_array_ref = \@seq_array; 
        # @seq_array is array of Seq objs
        $aln = $factory->align($seq_array_ref);
 Function: Perform a multiple sequence alignment
 Returns : Reference to a SimpleAlign object containing the
           sequence alignment.
 Args    : Name of a file containing a set of unaligned fasta sequences
           or else an array of references to Bio::Seq objects.
 Throws an exception if argument is not either a string (eg a
 filename) or a reference to an array of Bio::Seq objects.  If
 argument is string, throws exception if file corresponding to string
 name can not be found. If argument is Bio::Seq array, throws
 exception if less than two sequence objects are in array.
=cut
sub align {
    my ($self,$input) = @_;
    # Create input file pointer
    $self->io->_io_cleanup();
    my ($infilename) = $self->_setinput($input);
    if (! $infilename) {
        $self->throw("Bad input data or less than 2 sequences in $input !");
    }
    my $param_string = $self->_setparams($infilename);
    # run probcons
    return &_run($self, $param_string);
}
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=head2  _run
 Title   :  _run
 Usage   :  Internal function, not to be called directly        
 Function:  makes actual system call to probcons program
 Example :
 Returns : nothing; probcons output is written to a
           temporary file OR specified output file
 Args    : Name of a file containing a set of unaligned fasta sequences
           and hash of parameters to be passed to probcons
=cut
sub _run {
    my ($self, $params) = @_;
    my $commandstring = $self->executable." $params";
     
    $self->debug( "probcons command = $commandstring \n");
    my $status = system($commandstring);
    if ($status) {
        $self->warn( "Probcons call crashed: $? [command $commandstring]\n");
        return;
    }
     
    my $outfile = $self->outfile_name();
    if (-e $outfile || -z $outfile) {
        my $in  = Bio::AlignIO->new('-file'   => $outfile, 
                    '-format' => $self->aformat);
        my $aln = $in->next_aln();
        return $aln;
    }
    return; # some modes of operation do not generate an output alignment
}
HideShow 12 lines of Pod
=head2  _setinput
 Title   :  _setinput
 Usage   :  Internal function, not to be called directly        
 Function:  Create input file for probcons program
 Example :
 Returns : name of file containing probcons data input AND
 Args    : Arrayref of Seqs or input file name
=cut
sub _setinput {
    my ($self,$input) = @_;
    my ($infilename, $seq, $temp, $tfh);
    if (! ref $input) {
        # check that file exists or throw
        $infilename = $input;
        unless (-e $input) {return 0;}
        # let's peek and guess
        open(IN,$infilename) || $self->throw("Cannot open $infilename");
        my $header;
        while( defined ($header = <IN>) ) {
            last if $header !~ /^\s+$/;
        }
        close(IN);
        if ( $header !~ /^>\s*\S+/ ){
            $self->throw("Need to provide a FASTA format file to probcons!");
        } 
        return ($infilename);
    } elsif (ref($input) =~ /ARRAY/i ) { #  $input may be an
        #  array of BioSeq objects...
        #  Open temporary file for both reading & writing of array
        ($tfh,$infilename) = $self->io->tempfile();
        if( ! ref($input->[0]) ) {
            $self->warn("passed an array ref which did not contain objects to _setinput");
            return undef;
        } elsif( $input->[0]->isa('Bio::PrimarySeqI') ) {
            $temp =  Bio::SeqIO->new('-fh' => $tfh,
                                     '-format' => 'fasta');
            my $ct = 1;
            foreach $seq (@$input) {
                return 0 unless ( ref($seq) && 
                                  $seq->isa("Bio::PrimarySeqI") );
                if( ! defined $seq->display_id ||
                    $seq->display_id =~ /^\s+$/) {
                    $seq->display_id( "Seq".$ct++);
                } 
                $temp->write_seq($seq);
            }
            $temp->close();
            undef $temp;
            close($tfh);
            $tfh = undef;
        } else { 
            $self->warn( "got an array ref with 1st entry ".
                         $input->[0].
                         " and don't know what to do with it\n");
        }
        return ($infilename);
    } else { 
        $self->warn("Got $input and don't know what to do with it\n");
    }
    return 0;
}
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=head2  _setparams
 Title   :  _setparams
 Usage   :  Internal function, not to be called directly        
 Function:  Create parameter inputs for probcons program
 Example :
 Returns : parameter string to be passed to probcons
           during align or profile_align
 Args    : name of calling object
=cut
sub _setparams {
    my ($self, $infilename) = @_;
    my ($attr, $value,$param_string);
    $param_string = '';
    my $laststr;
    for  $attr ( @PROBCONS_PARAMS ) {
        $value = $self->$attr();
        next unless (defined $value);   
        my $attr_key = lc $attr;
        $attr_key = ' --'.$attr_key unless ($attr eq 'ANNOT');
        $attr_key = ' -'.$attr_key if ($attr eq 'ANNOT');
        $param_string .= $attr_key .' '.$value;
    }
    if ($self->{verbose_set}) {
        $param_string .= ' --verbose';
    }
    for  $attr ( @PROBCONS_SWITCHES) {
        $value = $self->$attr();
        next unless ($value);
        my $attr_key = lc $attr; #put switches in format expected by tcoffee
        $attr_key = ' -'.$attr_key;
        $param_string .= $attr_key ;
    }
    # Set default output file if no explicit output file selected
    unless ($self->outfile_name ) {  
        my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir());
        close($tfh);
        undef $tfh;
        $self->outfile_name($outfile);
    }
    #FIXME: This may be only for *nixes. Double check in other OSes
    $param_string .= " $infilename > ".$self->outfile_name;
     
    if ($self->verbose < 0) { 
        $param_string .= ' 2> /dev/null';
    }
    return $param_string;
}
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=head2 aformat
 Title   : aformat
 Usage   : my $alignmentformat = $self->aformat();
 Function: Get/Set alignment format
 Returns : string
 Args    : string
=cut
sub aformat{
    my $self = shift;
    $self->{'_aformat'} = shift if @_;
    return $self->{'_aformat'};
}
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=head1 Bio::Tools::Run::BaseWrapper methods
=cut
=head2 no_param_checks
 Title   : no_param_checks
 Usage   : $obj->no_param_checks($newval)
 Function: Boolean flag as to whether or not we should
           trust the sanity checks for parameter values  
 Returns : value of no_param_checks
 Args    : newvalue (optional)
=cut
=head2 save_tempfiles
 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Function: 
 Returns : value of save_tempfiles
 Args    : newvalue (optional)
=cut
=head2 outfile_name
 Title   : outfile_name
 Usage   : my $outfile = $probcons->outfile_name();
 Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
 Returns : string
 Args    : [optional] string to set value to
=cut
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=head2 tempdir
 Title   : tempdir
 Usage   : my $tmpdir = $self->tempdir();
 Function: Retrieve a temporary directory name (which is created)
 Returns : string which is the name of the temporary directory
 Args    : none
=cut
=head2 cleanup
 Title   : cleanup
 Usage   : $probcons->cleanup();
 Function: Will cleanup the tempdir directory
 Returns : none
 Args    : none
=cut
=head2 io
 Title   : io
 Usage   : $obj->io($newval)
 Function:  Gets a L<Bio::Root::IO> object
 Returns : L<Bio::Root::IO>
 Args    : none
=cut
1; # Needed to keep compiler happy