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Bio/Assembly/Tools/ContigSpectrum.pm  view on Meta::CPAN

  print "The contig spectrum from assembly is ".$from_assembly->to_string."\n";

  # Report advanced information (possible because eff_asm_params = 1)
  print "Average sequence length: ".$from_assembly->avg_seq_len." bp\n";
  print "Minimum overlap length: ".$from_assembly->min_overlap." bp\n";
  print "Average overlap length: ".$from_assembly->avg_overlap." bp\n";
  print "Minimum overlap match: ".$from_assembly->min_identity." %\n";
  print "Average overlap match: ".$from_assembly->avg_identity." %\n";

  # Assuming the assembly object contains sequences from several different
  # metagenomes, we have a mixed contig spectrum from which a cross contig
  # spectrum and dissolved contig spectra can be obtained
  my $mixed_csp = $from_assembly;

  # Calculate a dissolved contig spectrum
  my $meta1_dissolved = Bio::Assembly::Tools::ContigSpectrum->new(
    -dissolve => [$mixed_csp, 'metagenome1'] );
  my $meta2_dissolved = Bio::Assembly::Tools::ContigSpectrum->new(
    -dissolve => [$mixed_csp, 'metagenome2'] );
  print "The dissolved contig spectra are:\n".
    $meta1_dissolved->to_string."\n".
    $meta2_dissolved->to_string."\n";

  # Determine a cross contig spectrum
  my $cross_csp = Bio::Assembly::Tools::ContigSpectrum->new(
    -cross => $mixed_csp );
  print "The cross contig spectrum is ".$cross_csp->to_string."\n";

  # Score a contig spectrum (the more abundant the contigs and the larger their
  # size, the larger the score)
  my $csp_score = $csp->score( $csp->nof_seq );

=head1 DESCRIPTION

The Bio::Assembly::Tools::ContigSpectrum Perl module enables to
manually create contig spectra, import them from assemblies,
manipulate them, transform between different types of contig spectra
and output them.

Bio::Assembly::Tools::ContigSpectrum is a module to create, manipulate
and output contig spectra, assembly-derived data used in metagenomics
(community genomics) for diversity estimation.

=head2 Background

A contig spectrum is the count of the number of contigs of different
size in an assembly. For example, the contig spectrum [100 5 1 0 0
...] means that there were 100 singlets (1-contigs), 5 contigs of 2
sequences (2-contigs), 1 contig of 3 sequences (3-contig) and no
larger contigs.

An assembly can be produced from a mixture of sequences from different
metagenomes. The contig obtained from this assembly is a mixed contig
spectrum. The contribution of each metagenome in this mixed contig
spectrum can be obtained by determining a dissolved contig spectrum.

Finally, based on a mixed contig spectrum, a cross contig spectrum can
be determined. In a cross contig spectrum, only contigs containing
sequences from different metagenomes are kept; "pure" contigs are
excluded. Additionally, the total number of singletons (1-contigs)
from each region that assembles with any fragments from other regions
is the number of 1-contigs in the cross contig spectrum.

=head2 Implementation

The simplest representation of a contig spectrum is as a hash
representation where the key is the contig size (number of sequences
making up the contig) and the value the number of contigs of this
size.

In fact, it is useful to have more information associated with the
contig spectrum, hence the Bio::Assembly::Tools::ContigSpectrum module
implements an object containing a contig spectrum hash and additional
information. The get/set methods to access them are:

    id              contig spectrum ID
    nof_rep         number of repetitions (assemblies) used
    max_size        size of (number of sequences in) the largest contig
    spectrum        hash representation of a contig spectrum

    nof_seq         number of sequences
    avg_seq_len     average sequence length

    eff_asm_params  reports effective assembly parameters

    nof_overlaps    number of overlaps (needs eff_asm_params)
    min_overlap     minimum overlap length in a contig (needs eff_asm_params)
    min_identity    minimum sequence identity percentage (needs eff_asm_params)
    avg_overlap     average overlap length (needs eff_asm_params)
    avg_identity    average overlap identity percentage (needs eff_asm_params)

  Operations on the contig spectra:

    to_string       create a string representation of the spectrum
    spectrum        import a hash contig spectrum
    assembly        determine a contig spectrum from an assembly, contig or singlet
    dissolve        calculate a dissolved contig spectrum (depends on assembly)
    cross           produce a cross contig spectrum (depends on assembly)
    add             add a contig spectrum to an existing one
    average         make an average of several contig spectra
    score           score a contig spectrum: the higher the number of contigs
                      and the larger their size, the higher the score.

When using operations that rely on knowing "where" (from what
metagenomes) a sequence came from (i.e. when creating a dissolved or
cross contig spectrum), make sure that the sequences used for the
assembly have a name header, e.g.  E<gt>metagenome1|seq1,
E<gt>metagenome2|seq1, ...

Note: The following operations require the C<Graph::Undirected> module:
   eff_asm_params, cross, dissolve

=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 lists  Your participation is much appreciated.

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