Bio::Tools::Run::Phylo Gumby
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Summary
Bio::Tools::Run::Phylo::Gumby - Wrapper for gumby
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Tools::GFF
Bio::Tools::Phylo::Gumby
Bio::TreeIO
Cwd
File::Spec
Inherit
Bio::Tools::Run::Phylo::PhyloBase
Synopsis
  use Bio::Tools::Run::Phylo::Gumby;
# Make a Gumby factory $factory = Bio::Tools::Run::Phylo::Gumby->new(); # Run gumby with an alignment and tree file my @results = $factory->run($alignfilename, $treefilename); # or with alignment object and tree objects @results = $factory->run($bio_simplalign, $bio_tree_tree); # or with alignment object and Bio::DB::Taxonomy object @results = $factory->run($bio_simplalign, $bio_db_taxonomy); # specify the positions of exons in (at least) one of the alignment sequences # to get better results $factory->econs(1); $factory->annots($gff_filename); @results = $factory->run($alignfilename, $treefilename); # or using feature objects $factory->annots(@bio_seqfeature_objects); @results = $factory->run($alignfilename, $treefilename); # (mixtures of all the above are possible) # 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 gumby application by Shyam Prabhakar. You
can get details here: http://pga.lbl.gov/gumby/. Gumby is used for phylogenetic
footprinting/ shadowing.
You can try supplying normal gumby command-line arguments to new(), eg.
  $factory->new(-ratio => 2);
or calling arg-named methods (excluding the initial hyphen, eg.
  $factory->econs(1);
to set the -econs arg).
You will need to enable this Gumby wrapper to find the gumby program.
This can be done in (at least) three ways:
 1. Make sure the gumby executable is in your path.
2. Define an environmental variable GUMBYDIR which is a
directory which contains the gumby application:
In bash:
export GUMBYDIR=/home/username/gumby/ In csh/tcsh: setenv GUMBYDIR /home/username/gumby 3. Include a definition of an environmental variable GUMBYDIR in every script that will use this Gumby wrapper module, e.g.: BEGIN { $ENV{GUMBYDIR} = '/home/username/gumby/' } use Bio::Tools::Run::Phylo::Gumby;
Methods
program_nameDescriptionCode
program_dirDescriptionCode
newDescriptionCode
annotsDescriptionCode
runDescriptionCode
_run
No description
Code
_setparamsDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns : string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args : None
newcodeprevnextTop
 Title   : new
Usage : $factory = Bio::Tools::Run::Phylo::Gumby->new()
Function: creates a new Gumby factory
Returns : Bio::Tools::Run::Phylo::Gumby
Args : Most options understood by gumby can be supplied as key =>
value pairs.
These options can NOT be used with this wrapper: o minseq blklen
annotscodeprevnextTop
 Title   : annots
Usage : $factory->annots(@gff_filenames)
Function: Specify annotation files for gumby to use
Returns : string of absolute filepaths to gff files
Args : list of gff filenames (can be relative), where the first column
corresponds to a sequence id from the alignment that will be supplied
to run()
OR
list of Bio::SeqFeatureI objects, which have seq_id() values that
will correspond to the sequence ids from the alignment that will
be supplied to run() (the objects will be grouped by seq_id and
output to gff files for use by gumby; filepaths to those tempfiles
will be returned). Note that all features must have source, seq_id
and primary_tag set or none will be used.
NB: feature coordinates must be relative to the parts of the sequences in the alignment you will supply, as though numbering started at 1 for each each sequence in the alignment. There is currently no automatic correction for this.
runcodeprevnextTop
 Title   : run
Usage : $result = $factory->run($fasta_align_file, $newick_tree_file);
-or-
$result = $factory->run($align_object, $tree_object);
-or-
$result = $factory->run($align_object, $db_taxonomy_object);
Function: Runs gumby on an alignment.
Returns : list of Bio::SeqFeature::Annotated (one per prediction and sequence)
Args : The first argument represents an alignment, the second argument
a species tree.
The alignment can be provided as a multi-fasta format alignment
filename, or a Bio::Align::AlignI complient object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
or a Bio::Tree::TreeI complient object. Alternatively a
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
In all cases, the alignment sequence names must correspond to node ids in the species tree. Multi-word species names should have the spaces removed to form the sequence names, eg. Homosapiens. Underscores may also be used for either or both of sequence and node ids ('Homo_sapiens'), but underscores will be removed internally. NB: Gumby treats each sequence in the alignment as starting at position 1. This method returns results with the coordinates corrected so they match the coordinates of your input alignment. Eg. if 'Homo_sapiens' sequence had the range 20..60 in your alignment, the first Gumby result might be 1..5 which is corrected to 20..24.
_setparamscodeprevnextTop
 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
Methods code
program_namedescriptionprevnextTop
sub program_name {
    return $PROGRAM_NAME;
}
program_dirdescriptionprevnextTop
sub program_dir {
    return $PROGRAM_DIR;
}
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    $self->_set_from_args(\@args, -methods => [@PARAMS, @SWITCHES, 'quiet'],
                                  -create => 1);
    
    return $self;
}
annotsdescriptionprevnextTop
sub annots {
    my $self = shift;
    if (@_) {
        my @files;
        my %feats;
        foreach my $thing (@_) {
            if (ref($thing) && $thing->isa('Bio::SeqFeatureI')) {
                my $seq_id = $thing->seq_id || $self->throw("Supplied a feature with no seq_id");
                push(@{$feats{$seq_id}}, $thing);
            }
            elsif (-e $thing) {
                push(@files, File::Spec->rel2abs($thing));
            }
            else {
                $self->throw("'$thing' was not a Bio::SeqFeatureI or a file");
            }
        }
        
        if (keys %feats) {
            my $temp_dir = $self->tempdir;
            
            while (my ($seq_id, $feats) = each %feats) {
                my $temp_file = File::Spec->catfile($temp_dir, $seq_id.'.gff');
                $temp_file = File::Spec->rel2abs($temp_file);
                my $gffout = Bio::Tools::GFF->new(-file => ">$temp_file", -gff_version => 2);
                $gffout->write_feature(@{$feats});
                push(@files, $temp_file);
            }
        }
        
        $self->{annots} =\@ files;
    }
    
    if (defined $self->{annots}) {
        return join(' ', @{$self->{annots}});
    }
    return;
}
rundescriptionprevnextTop
sub run {
    my ($self, $aln, $tree) = @_;
    
    ($aln && $tree) || $self->throw("alignment and tree must be supplied");
    $aln = $self->_alignment($aln);
    $tree = $self->_tree($tree);
    
    $tree->force_binary;
    
    # adjust seq & node ids to remove spaces and underscores (eg. if tree
# generated from taxonomy/ user input bad names)
foreach my $thing ($tree->get_leaf_nodes, $aln->each_seq) { my $id = $thing->id; $id =~ s/_aligned//; #*** dubious custom-handling for the allowed case of mlagan adding _aligned to id (according to gumby author)
$id =~ s/[ _]//g; $thing->id($id); } my $new_aln = $aln->new; foreach my $seq ($aln->each_seq) { $new_aln->add_seq($seq); } $self->_alignment($new_aln); #*** at some stage we want to revert the ids back to original...
# check node and seq names match
$self->_check_names; return $self->_run;
}
_rundescriptionprevnextTop
sub _run {
    my $self = shift;
    
    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 $tree_file = 'tree_file'; my $aln_file = $self->_write_alignment; # generate a gumby-friendly tree file
my $tree = $self->_tree; $tree = $tree->simplify_to_leaves_string; open(my $tfhandle, '>', $tree_file) || $self->throw("Could not write to tree file '$tree_file'"); print $tfhandle $tree, "\n"; close($tfhandle); my $command = $exe.$self->_setparams($aln_file, $tree_file); $self->debug("gumby command = $command\n"); open(PIPE, "$command |") || $self->throw("gumby call ($command) failed to start: $? | $!"); my $error = ''; while (<PIPE>) { print unless $self->quiet; if (/^ERROR: (.+)/ || /^mbgumbel\(\): (.+)/) { $error .= $1; } } close(PIPE) || ($error ? $self->warn("gumby call ($command) failed: $error") : $self->throw("gumby call ($command) crashed: $?")); my $aln = $self->_alignment(); my %offsets; foreach my $seq ($aln->each_seq) { $offsets{lc($seq->id)} = $seq->start - 1; } my @feats = (); foreach my $file ('out_all.align', 'out_exon.align', 'out_nonexon.align') { -e $file || next; my $parser = Bio::Tools::Phylo::Gumby->new(-file => $file); while (my @results = $parser->next_result) { foreach my $result (@results) { my $this_adjust = $offsets{lc($result->seq_id)}; $result->start($result->start + $this_adjust); $result->end($result->end + $this_adjust); } push(@feats, @results); } unlink($file); } # cd back again
chdir($cwd) || $self->throw("Couldn't change back to working directory '$cwd'"); return @feats;
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($self, $aln_file, $tree_file) = @_;
    
    my $param_string = ' '.$tree_file;
    $param_string .= ' '.$aln_file;
    $param_string .= $self->SUPER::_setparams(-params =>\@ PARAMS,
                                              -switches =>\@ SWITCHES,
                                              -dash => 1,);
    $param_string .= ' -o out';
    $param_string .= ' 2>&1';
    $param_string .= ' 1>/dev/null' if $self->quiet;
    
    return $param_string;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
 
Please direct usage questions or support issues to the mailing list:

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.
Reporting BugsTop
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://bugzilla.open-bio.org/
AUTHOR - Sendu BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _