Bio::Assembly IO
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Summary
Bio::Assembly::IO - Handler for Assembly::IO Formats
Package variables
No package variables defined.
Inherit
Bio::Root::IO Bio::Root::Root
Synopsis
    use Bio::Assembly::IO;

    $in  = Bio::Assembly::IO->new(-file=>"'phrap');
    $out = Bio::Assembly::IO->new(-file=>">outputfilename",
                                  -format=>'phrap');

    while ( my $scaffold = $in->next_assembly() ) {
       # do something with Bio::Assembly::Scaffold instance
       # ...
       $out->write_assembly(-scaffold => $scaffold);
    }

    $in->close;
    $out->close;
Description
Bio::Assembly::IO is a handler module for formats in the Assembly::IO set
(e.g. Bio::Assembly::IO::phrap).
Methods
newDescriptionCode
_initialize
No description
Code
next_assemblyDescriptionCode
next_contigDescriptionCode
write_assemblyDescriptionCode
write_headerDescriptionCode
write_contigDescriptionCode
write_footerDescriptionCode
_load_format_moduleDescriptionCode
_guess_formatDescriptionCode
_sortDescriptionCode
DESTROY
No description
Code
TIEHANDLE
No description
Code
READLINE
No description
Code
PRINT
No description
Code
Methods description
newcode    nextTop
 Title   : new
 Usage   : $stream = Bio::Assembly::IO->new( -file   => $filename,
                                             -format =>'format'    )
 Function: Returns a new assembly stream
 Returns : A Bio::Assembly::IO::Handler initialised
           with the appropriate format
 Args    : -file   => $filename
           -format => format
next_assemblycodeprevnextTop
 Title   : next_assembly
 Usage   : $scaffold = $stream->next_assembly()
 Function: Reads the next assembly object from the stream and returns it.
 Returns : a Bio::Assembly::ScaffoldI compliant object
 Args    : none
next_contigcodeprevnextTop
 Title   : next_contig
 Usage   : $contig = $stream->next_contig()
 Function: Reads the next contig or singlet from the stream and returns it.
 Returns : a Bio::Assembly::Contig or Bio::Contig::Assembly::Singlet
 Args    : none
write_assemblycodeprevnextTop
  Title   : write_assembly
  Usage   : $stream->write_assembly($assembly)
  Function: Write the assembly object in desired format. This method calls
            write_header(), write_contigs() and write_footer() internally.
  Returns : 1 on success, 0 for error
  Args    : A Bio::Assembly::Scaffold object
write_headercodeprevnextTop
  Title   : write_header
  Usage   : $stream->write_header($assembly)
  Function: Write the start of the assembly file. It can be called at any time,
            not when starting to write the assembly file. 
  Returns : 1 on success, 0 for error
  Args    : A Bio::Assembly::Scaffold object or ... (check the specific format
            driver for more details)
write_contigcodeprevnextTop
  Title   : write_contig
  Usage   : $stream->write_contig($contig)
  Function: Write a contig object in the desired format.
  Returns : 1 on success, 0 for error
  Args    : A Bio::Assembly::Contig object
write_footercodeprevnextTop
  Title   : write_footer
  Usage   : $stream->write_footer($assembly)
  Function: Write the start of the assembly file.
  Returns : 1 on success, 0 for error
  Args    : A Bio::Assembly::Scaffold object or ... (check the specific format
            driver for more details)
_load_format_modulecodeprevnextTop
 Title   : _load_format_module
 Usage   : *INTERNAL Assembly::IO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :
_guess_formatcodeprevnextTop
 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function: guess format based on file suffix
 Example :
 Returns : guessed format of filename (lower case)
 Args    :
 Notes   : formats that _filehandle() will guess includes
           ace, phrap and tigr at the moment
_sortcodeprevnextTop
    Title   : _sort
    Usage   : @sorted_values = $ass_io->_sort(@values)
    Function: Sort a list of values naturally if Sort::Naturally is installed
              (nicer), lexically otherwise (not as nice, but safe)
    Returns : array of sorted values
    Args    : array of values to sort
Methods code
newdescriptionprevnextTop
sub new {
    my ($caller,@args) = @_;
    my $class = ref($caller) || $caller;

    # or do we want to call SUPER on an object if $caller is an
    # object?
    if( $class =~ /Bio::Assembly::IO::(\S+)/ ) {
        my ($self) = $class->SUPER::new(@args);
        $self->_initialize(@args);
        return $self;
    } else {

        my %param = @args;
        @param{ map { lc $_ } keys %param } = values %param; # lowercase keys

        $class->throw("Need at least a file name to proceed!")
            unless (defined $param{'-file'} || defined $ARGV[0]);

        my $format = $param{'-format'} ||
        $class->_guess_format( $param{-file} || $ARGV[0] );
        $format = "\L$format";	# normalize capitalization to lower case

        if ($format =~ /-/) {
            ($format, my $variant) = split('-', $format, 2);
            push @args, (-variant => $variant);
        }

        return unless( $class->_load_format_module($format) );
        return "Bio::Assembly::IO::$format"->new(@args);
    }
}
_initializedescriptionprevnextTop
sub _initialize {
    my($self, @args) = @_;
    # initialize the IO part
    $self->_initialize_io(@args);
}
next_assemblydescriptionprevnextTop
sub next_assembly {
   my ($self) = @_;
   $self->throw("Cannot read from a generic Bio::Assembly::IO object.");
}
next_contigdescriptionprevnextTop
sub next_contig {
   my ($self) = @_;
   $self->throw("Cannot read from a generic Bio::Assembly::IO object.");
}
write_assemblydescriptionprevnextTop
sub write_assembly {
    my ($self, @args) = @_;
    my ($scaf, $write_singlets) = $self->_rearrange([qw(SCAFFOLD SINGLETS)], @args);

    # Sanity check
    if ( !$scaf || !$scaf->isa('Bio::Assembly::ScaffoldI') ) {
        $self->throw("Must provide a Bio::Assembly::Scaffold object when calling write_assembly");
    }

    # Write header
    $self->write_header($scaf);

    # ID-sorted contig and read entries
    my @contig_ids  = $scaf->get_contig_ids;
    if ($write_singlets) {
        push @contig_ids, $scaf->get_singlet_ids;
    }
    @contig_ids = _sort(@contig_ids);

    # Write contigs
    for my $contig_id ( @contig_ids ) {
        my $contig = $scaf->get_contig_by_id($contig_id) ||
                     $scaf->get_singlet_by_id($contig_id);
        $self->write_contig($contig);
    }

    # Write footer
    $self->write_footer($scaf);

    return 1;
}
write_headerdescriptionprevnextTop
sub write_header {
   my ($self) = @_;
   $self->throw("Cannot write from a generic Bio::Assembly::IO object.");
}
write_contigdescriptionprevnextTop
sub write_contig {
   my ($self) = @_;
   $self->throw("Cannot write from a generic Bio::Assembly::IO object.");
}
write_footerdescriptionprevnextTop
sub write_footer {
   my ($self) = @_;
   $self->throw("Cannot write from a generic Bio::Assembly::IO object.");
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
  my ($self,$format) = @_;
  my $module = "Bio::Assembly::IO::" . $format;
  my $ok;

  eval {
      $ok = $self->_load_module($module);
  };
  if ( $@ ) {
    print STDERR <<END;
$self: could not load $format - for more details on supported formats please see the Assembly::IO docs
Exception $@
END
  ;
  }
  return $ok;
}
_guess_formatdescriptionprevnextTop
sub _guess_format {
   my $class = shift;
   my $arg   = shift;

   return unless defined($arg);
   return 'ace'    if ($arg =~ /\.ace/i);
   return 'phrap'  if ($arg =~ /\.phrap/i);
   return 'tigr'   if ($arg =~ /\.tigr/i);
   return 'maq'    if ($arg =~ /\.maq/i);
   return 'sam'    if ($arg =~ /\.[bs]am/i);
   return 'bowtie' if ($arg =~ /\.bowtie/i);
}
_sortdescriptionprevnextTop
sub _sort {
    my @arr = @_;
    my @sorted_arr;
    if (eval { require Sort::Naturally }) {
        @sorted_arr = Sort::Naturally::nsort( @arr ); # natural sort (better)
    } else {
        @sorted_arr = sort @arr; # lexical sort (safe)
    }
    return @sorted_arr;
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;

    $self->close();
}

# I need some direction on these!! The module works so I haven't fiddled with them!
# Me neither! (rfsouza)
}
TIEHANDLEdescriptionprevnextTop
sub TIEHANDLE {
    my ($class,$val) = @_;
    return bless {'seqio' => $val}, $class;
}
READLINEdescriptionprevnextTop
sub READLINE {
    my $self = shift;
    return $self->{'seqio'}->next_seq() unless wantarray;
    my (@list, $obj);
    push @list, $obj while $obj = $self->{'seqio'}->next_seq();
    return @list;
}
PRINTdescriptionprevnextTop
sub PRINT {
    my $self = shift;
    $self->{'seqio'}->write_seq(@_);
}

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 lists 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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Robson Francisco de Souza
E-mail: rfsouza@citri.iq.usp.br
CONTRIBUTORSTop
#
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
formatTop
 Title   : format
 Usage   : $format = $stream->format()
 Function: Get the assembly format
 Returns : assembly format
 Args    : none