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Summary

Bio::Tools::Run::MCS - Wrapper for MCS

Package variables

Included modules

Inherit

Bio::Tools::Run::Phylo::PhyloBase

Synopsis

  use Bio::Tools::Run::MCS;

  # Make a MCS factory
  $factory = Bio::Tools::Run::MCS->new();

  # Run MCS on an alignment
  my @results = $factory->run($alignfilename);

  # or with alignment object
  @results = $factory->run($bio_simplalign);

  # look at the results
  foreach my $feat (@results) {
    my $seq_id = $feat->seq_id;
    my $start = $feat->start;
    my $end = $feat->end;
    my $score = $feat->score;
    my ($pvalue) = $feat->get_tag_values('pvalue');
    my ($kind) = $feat->get_tag_values('kind'); # 'all', 'exon' or 'nonexon'
  }

Description

This is a wrapper for running the MCS (binCons) scripts by Elliott H Margulies.
You can get details here: http://zoo.nhgri.nih.gov/elliott/mcs_doc/. MCS is used
for the prediciton of transcription factor binding sites and other regions of
the genome conserved amongst different species.
Note that this wrapper assumes you already have alignments, so only uses MCS
for the latter stages (the stages involving align2binomial.pl,
generate_phyloMAX_score.pl and generate_mcs_beta.pl).
You can try supplying normal MCS command-line arguments to new(), eg.

  $factory->new(-percentile => 95)

or calling arg-named methods (excluding the initial
hyphens, eg.

  $factory->percentile(95)

 to set the --percentile arg).

You will need to enable this MCS wrapper to find the MCS scripts.
This can be done in (at least) three ways:

 1. Make sure the MCS scripts are in your path.
 2. Define an environmental variable MCSDIR which is a 
    directory which contains the MCS scripts:
    In bash:

    export MCSDIR=/home/username/mcs/

    In csh/tcsh:

    setenv MCSDIR /home/username/mcs

 3. Include a definition of an environmental variable MCSDIR in
    every script that will use this MCS wrapper module, e.g.:

    BEGIN { $ENV{MCSDIR} = '/home/username/mcs/' }
    use Bio::Tools::Run::MCS;

Methods

Methods description

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns : string
 Args    : None

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns : string
 Args    : None

 Title   : new
 Usage   : $factory = Bio::Tools::Run::MCS->new()
 Function: creates a new MCS factory
 Returns : Bio::Tools::Run::MCS
 Args    : Many options understood by MCS can be supplied as key =>
           value pairs.

           These options can NOT be used with this wrapper:
           ucsc gtf neutral-only fourd-align align-only ar

 Title   : run
 Usage   : $result = $factory->run($align_file_or_object, Bio::Location::Atomic,
                                   [Bio::SeqFeatureI]);
 Function: Runs the MCS scripts on an alignment.
 Returns : list of Bio::SeqFeatureI feature objects (with coordinates corrected
           according to the supplied offset, if any)
 Args    : The first argument represents an alignment, the optional second
           argument represents the chromosome, stand and end and the optional
           third argument represents annotation of the exons in the alignment.

           The alignment can be provided as a multi-fasta format alignment
           filename, or a Bio::Align::AlignI compliant object (eg. a
           Bio::SimpleAlign).

           The position in the genome can be provided as a Bio::Location::Atomic
           with start, end and seq_id set.

           The annnotation can be provided as an array of Bio::SeqFeatureI
           objects.

 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    : none

Methods code

BEGIN {

    # lets add all the mcs scripts to the path so that when we call
    # align2binomial.pl it can find its siblings
    $PROGRAM_DIR = $ENV{'MCSDIR'};
    $ENV{PATH} = "$PROGRAM_DIR:$ENV{PATH}" if $PROGRAM_DIR;

}

sub program_name {

    return $PROGRAM_NAME;

}

sub program_dir {

    return $PROGRAM_DIR;

}

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    $self->_set_from_args(\@args, -methods => [@PARAMS, @SWITCHES, 'quiet'],
                                  -create => 1);
    
    return $self;

}

sub run {

    my ($self, $aln, $offset, $exon_feats) = @_;
    $self->_alignment($aln || $self->alignment || $self->throw("An alignment must be supplied"));
    
    return $self->_run($offset, $exon_feats);

}

sub _run {

    my ($self, $atomic, $exon_feats) = @_;
    
    my $exe = $self->executable || return;
    
    # cd to a temp dir
    my $temp_dir = $self->tempdir;
    my $cwd = Cwd->cwd();
    chdir($temp_dir) || $self->throw("Couldn't change to temp dir '$temp_dir'");
    
    my $offset = '';
    my $start_adjust = 0;
    if ($atomic) {
        $start_adjust = $atomic->start;
        $offset = '--ucsc '.$atomic->seq_id.':'.$start_adjust.'-'.$atomic->end;
        $start_adjust--;
    }
    
    my $gtf_file = 'exons.gtf';
    if ($exon_feats) {
        my $fout = Bio::FeatureIO->new(-file => ">$gtf_file", -format => 'gtf');
        foreach my $feat (@{$exon_feats}) {
            $fout->write_feature($feat);
        }
    }
    my $gtf = $exon_feats ? "--gtf $gtf_file" : '';
    
    # step '2' (http://zoo.nhgri.nih.gov/elliott/mcs_doc/node1.html) of MCS:
    # run align2binomial.pl to calculate individual species binomial scores
    my $aln_file = $self->_write_alignment;
    my $error_file = 'stderr';
    my $binomial_file = 'align_name.binomial';
    my $cmd = "align2binomial.pl $offset $gtf $aln_file > $binomial_file 2> $error_file";
    #system("rm -fr $cwd/mcs_dir; cp -R $temp_dir $cwd/mcs_dir");
    my $throw = system($cmd);
    open(my $efh, "<", $error_file) || $self->throw("Could not open error file '$error_file'");
    my $error;
    while (<$efh>) {
        $error .= $_;
        $throw = 1 if /not divisible by 3/;
    }
    close($efh);
    $self->throw($error) if $throw;
    
    # step '3': run generate_phyloMAX_score.pl to combine the individual
    # binomial scores and generate the final Multi-species Conservation Score
    my $phylo_file = 'align_name.phylo';
    system("generate_phyloMAX_score.pl $binomial_file > $phylo_file") && $self->throw("generate_phyloMAX_score.pl call failed: $?, $!");
    
    # step '4': Generate MCSs from the conservation score using
    # generate_mcs_beta.pl
    my $mcs_file = 'mcs_result.stdout';
    my $bed_file = 'align_name.bed'; # hardcoded in generate_mcs_beta.pl
    system("generate_mcs_beta.pl $offset $gtf $phylo_file > $mcs_file") && $self->throw("generate_mcs_beta.pl failed: $?, $!");
    
    my @feats;
    my $fin = Bio::FeatureIO->new(-file => $bed_file, -format => 'bed');
    my $source = Bio::Annotation::SimpleValue->new(-value => 'MCS');
    while (my $feat = $fin->next_feature()) {
        # convert coords given offset
        if ($start_adjust) {
            $feat->start($feat->start + $start_adjust);
            $feat->end($feat->end + $start_adjust);
        }
        $feat->source($source);
        push(@feats, $feat);
    }
    
    # cd back again
    chdir($cwd) || $self->throw("Couldn't change back to working directory '$cwd'");
    
    return @feats;

}

sub _setparams {

    my $self = shift;
    
    my $param_string = $self->SUPER::_setparams(-params =>\@ PARAMS,
                                           -switches =>\@ SWITCHES,
                                           -dash => 1);
    
    $param_string .= ' 1>/dev/null' if $self->quiet;
    
    return $param_string;
}

1;

}

General documentation

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with code and data examples if at all possible.

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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _