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BioPerl-1.007000_004
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/ Bio::Assembly::Tools::ContigSpectrum

NAME

Bio::Assembly::Tools::ContigSpectrum - create and manipulate contig spectra

SYNOPSIS

# Simple contig spectrum creation
my $csp1 = Bio::Assembly::Tools::ContigSpectrum->new(
  -id       => 'csp1',
  -spectrum => { 1 => 10,
                 2 => 2,
                 3 => 1 } );

# ...or another way to create a simple contig spectrum
my $csp2 = Bio::Assembly::Tools::ContigSpectrum->new;
$csp2->id('csp2');
$csp2->spectrum({ 1 => 20, 2 => 1, 4 => 1 });

# Get some information
print "This is contig spectrum ".$csp->id."\n";
print "It contains ".$csp->nof_seq." sequences\n";
print "The largest contig has ".$csp->max_size." sequences\n";
print "The spectrum is: ".$csp->to_string($csp->spectrum)."\n";

# Let's add the contig spectra
my $summed_csp = Bio::Assembly::Tools::ContigSpectrum->new;
$summed_csp->add($csp1);
$summed_csp->add($csp2);
print "The summed contig spectrum is ".$summed_csp->to_string."\n";

# Make an average
my $avg_csp = Bio::Assembly::Tools::ContigSpectrum->new;
$avg_csp = $avg_csp->average([$csp1, $csp2]);
print "The average contig spectrum is ".$avg_csp->to_string."\n";

# Get a contig spectrum from an assembly
my $from_assembly = Bio::Assembly::Tools::ContigSpectrum->new(
  -assembly       => $assembly_object,
  -eff_asm_params => 1);
print "The contig spectrum from assembly is ".$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 );

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.

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.

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. >metagenome1|seq1, >metagenome2|seq1, ...

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

FEEDBACK

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.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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 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 email or the web:

bioperl-bugs@bio.perl.org
https://github.com/bioperl/bioperl-live/issues

AUTHOR - Florent E Angly

Email florent_dot_angly_at_gmail_dot_com

APPENDIX

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

new

Title   : new
Usage   : my $csp = Bio::Assembly::Tools::ContigSpectrum->new();
            or
          my $csp = Bio::Assembly::Tools::ContigSpectrum->new(
            -id => 'some_name',
            -spectrum =>  { 1 => 90 , 2 => 3 , 4 => 1 },
          );
            or
          my $csp = Bio::Assembly::Tools::ContigSpectrum->new(
            -assembly =>  $assembly_obj
          );
Function: create a new contig spectrum object
Returns : reference to a contig spectrum object
Args    : none

id

Title   : id
Usage   : $csp->id
Function: get/set contig spectrum id
Returns : string
Args    : string [optional]

nof_seq

Title   : nof_seq
Usage   : $csp->nof_seq
Function: get/set the number of sequences making up the contig spectrum
Returns : integer
Args    : integer [optional]

nof_rep

Title   : nof_rep
Usage   : $csp->nof_rep
Function: Get/Set the number of repetitions (assemblies) used to create the 
          contig spectrum
Returns : integer
Args    : integer [optional]

max_size

Title   : max_size
Usage   : $csp->max_size
Function: get/set the size of (number of sequences in) the largest contig
Returns : integer
Args    : integer [optional]

nof_overlaps

Title   : nof_overlaps
Usage   : $csp->nof_overlaps
Function: Get/Set the number of overlaps in the assembly.
Returns : integer
Args    : integer [optional]

min_overlap

Title   : min_overlap
Usage   : $csp->min_overlap
Function: get/set the assembly minimum overlap length
Returns : integer
Args    : integer [optional]

avg_overlap

Title   : avg_overlap
Usage   : $csp->avg_overlap
Function: get/set the assembly average overlap length
Returns : decimal
Args    : decimal [optional]

min_identity

Title   : min_identity
Usage   : $csp->min_identity
Function: get/set the assembly minimum overlap identity percent
Returns : 0 < decimal < 100
Args    : 0 < decimal < 100 [optional]

avg_identity

Title   : avg_identity
Usage   : $csp->avg_identity
Function: get/set the assembly average overlap identity percent
Returns : 0 < decimal < 100
Args    : 0 < decimal < 100 [optional]

avg_seq_len

Title   : avg_seq_len
Usage   : $csp->avg_seq_len
Function: get/set the assembly average sequence length
Returns : avg_seq_len
Args    : real [optional]

eff_asm_params

Title   : eff_asm_params
Usage   : $csp->eff_asm_params(1)
Function: Get/set the effective assembly parameters option. It defines if the
          effective assembly parameters should be determined when a contig
          spectrum based or derived from an assembly is calculated. The
          effective assembly parameters include avg_seq_length, nof_overlaps,
          min_overlap, avg_overlap, min_identity and avg_identity.
          1 = get them, 0 = don't.
Returns : integer
Args    : integer [optional]

spectrum

Title   : spectrum
Usage   : my $spectrum = $csp->spectrum({1=>10, 2=>2, 3=>1});
Function: Get the current contig spectrum represented as a hash / Update a
          contig spectrum object based on a contig spectrum represented as a
          hash
          The hash representation of a contig spectrum is as following:
            key   -> contig size (in number of sequences)
            value -> number of contigs of this size
Returns : contig spectrum as a hash reference
Args    : contig spectrum as a hash reference [optional]

assembly

Title   : assembly
Usage   : my @obj_list = $csp->assembly();
Function: get/set the contig spectrum object by adding an assembly, contig or
          singlet object to it, or get the list of objects associated with it
Returns : arrayref of assembly, contig and singlet objects used in the contig
          spectrum object (Bio::Assembly::Scaffold, Bio::Assembly::Contig and
          Bio::Assembly::Singlet objects)
Args    : Bio::Assembly::Scaffold, Contig or Singlet object

drop_assembly

Title   : drop_assembly
Usage   : $csp->drop_assembly();
Function: Remove all assembly objects associated with a contig spectrum.
          Assembly objects can take a lot of memory, which can be freed by
          calling this method. Don't call this method if you need the assembly
          object later on, for example for creating a dissolved or cross
          contig spectrum.
Returns : 1 for success
Args    : none

dissolve

Title   : dissolve
Usage   : $dissolved_csp->dissolve($mixed_csp, $seq_header);
Function: Dissolve a mixed contig spectrum for the set of sequences that
          contain the specified header, i.e. determine the contribution of
          these sequences to the mixed contig spectrum. The mixed contig
          spectrum object must have one or several assembly object(s). In
          addition, min_overlap, min_identity and eff_asm_params are taken
          from the mixed contig spectrum, unless they are specified manually
          for the dissolved contig spectrum. The dissolved contigs underlying
          the contig spectrum can be obtained by calling the assembly() method.
Returns : 1 for success
Args    : Bio::Assembly::Tools::ContigSpectrum reference
          sequence header string

cross

Title   : cross
Usage   : $cross_csp->cross($mixed_csp);
Function: Calculate a cross contig_spectrum based on a mixed contig_spectrum.
          The underlying cross-contigs themselves can be obtained by calling 
          the assembly() method.
Returns : 1 for success
Args    : Bio::Assembly::Tools::ContigSpectrum reference

to_string

Title   : to_string
Usage   : my $csp_string = $csp->to_string;
Function: Convert the contig spectrum into a string (easy to print!!).
Returns : string
Args    : element separator (integer) [optional]
            1 -> space-separated
            2 -> tab-separated
            3 -> newline-separated

add

Title   : add
Usage   : $csp->add($additional_csp);
Function: Add a contig spectrum to an existing one: sums the spectra, update
          the number of sequences, number of repetitions, ...
Returns : 1 for success
Args    : Bio::Assembly::Tools::ContigSpectrum object

average

Title   : average
Usage   : my $avg_csp = $csp->average([$csp1, $csp2, $csp3]);
Function: Average one contig spectrum or the sum of several contig spectra by
          the number of repetitions
Returns : Bio::Assembly::Tools::ContigSpectrum
Args    : Bio::Assembly::Tools::ContigSpectrum array reference
          eff_asm_params

score

Title   : score
Usage   : my $score = $csp->score();
Function: Score a contig spectrum (or cross-contig spectrum) such that the
           higher the number of contigs (or cross-contigs) and the larger their 
           size, the higher the score.
           Let n   : total number of sequences
               c_q : number of contigs of size q
               q   : number of sequence in a contig
           We define: score = n/(n-1) * (X - 1/n)
                where X = sum ( c_q * q^2 ) / n**2
           The score ranges from 0 (singlets only) to 1 (a single large contig)
           It is possible to specify a value for the number of sequences to
            assume in the contig spectrum.
Returns : contig score, or undef if there were no sequences in the contig spectrum
Args    : number of total sequences to assume [optional]

_naive_assembler

Title   : _naive_assembler
Usage   : 
Function: Reassemble the specified sequences only based on their position in
          the contig. This naive assembly only verifies that the minimum
          overlap length and percentage identity are respected. No actual
          alignment is done
Returns : arrayref of contigs and singlets
Args    : Bio::Assembly::Contig
          array reference of sequence IDs to use [optional]
          minimum overlap length (integer)       [optional]
          minimum percentage identity (integer)  [optional]

_create_subcontig

Title   : _create_subcontig
Usage   : 
Function: Create a subcontig from another contig
Returns : Bio::Assembly::Contig object
Args    : Bio::Assembly::Contig
          arrayref of the IDs of the reads to includes in the subcontig
          ID to give to the subcontig

_obj_copy

Title   : _obj_copy
Usage   : 
Function: Copy (most of) an object, and optionally truncate it
Returns : another a Bio::LocatableSeq, Bio::Seq::PrimaryQual, or
            Bio::SeqFeature::Generic object
Args    : a Bio::LocatableSeq, Bio::Seq::PrimaryQual, or
            Bio::SeqFeature::Generic object
          a start position
          an end position

_new_from_assembly

Title   : _new_from_assembly
Usage   : 
Function: Creates a new contig spectrum object based solely on the result of 
          an assembly, contig or singlet
Returns : Bio::Assembly::Tools::ContigSpectrum object
Args    : Bio::Assembly::Scaffold, Contig or Singlet object

_new_dissolved_csp

Title   : _new_dissolved_csp
Usage   : 
Function: create a dissolved contig spectrum object
Returns : dissolved contig spectrum
Args    : mixed contig spectrum
          header of sequences to keep in this contig spectrum

_dissolve_contig

Title   : _dissolve_contig
Usage   : 
Function: dissolve a contig
Returns : arrayref of contigs and singlets
Args    : mixed contig spectrum
          header of sequences to keep in this contig spectrum
          minimum overlap
          minimum identity

_new_cross_csp

Title   : _new_cross_csp
Usage   : 
Function: create a cross contig spectrum object
Returns : cross-contig spectrum
Args    : mixed contig spectrum

_cross_contig

Title   : _cross_contig
Usage   : 
Function: calculate cross contigs
Returns : arrayref of cross-contigs
          number of cross-singlets
Args    : contig
          minimum overlap
          minimum identity

_seq_origin

Title   : _seq_origin
Usage   : 
Function: determines where a sequence comes from using its header. For example
          the origin of the sequence 'metagenome1|gi|9626988|ref|NC_001508.1|'
          is 'metagenome1'
Returns : origin
Args    : sequence ID

_import_assembly

Title   : _import_assembly
Usage   : $csp->_import_assembly($assemblyobj);
Function: Update a contig spectrum object based on an assembly, contig or
          singlet object
Returns : 1 for success
Args    : Bio::Assembly::Scaffold, Contig or Singlet object

_import_spectrum

Title   : _import_spectrum
Usage   : $csp->_import_spectrum({ 1 => 90 , 2 => 3 , 4 => 1 })
Function: update a contig spectrum object based on a contig spectrum
          represented as a hash (key: contig size, value: number of contigs of
          this size)
Returns : 1 for success
Args    : contig spectrum as a hash reference

_import_dissolved_csp

Title   : _import_dissolved_csp
Usage   : $csp->_import_dissolved_csp($mixed_csp, $seq_header);
Function: Update a contig spectrum object by dissolving a mixed contig
          spectrum based on the header of the sequences
Returns : 1 for success
Args    : Bio::Assembly::Tools::ContigSpectrum
          sequence header string

_import_cross_csp

Title   : _import_cross_csp
Usage   : $csp->_import_cross_csp($mixed_csp);
Function: Update a contig spectrum object by calculating the cross contig
          spectrum based on a mixed contig spectrum
Returns : 1 for success
Args    : Bio::Assembly::Tools::ContigSpectrum

_get_contig_like

Title   : _get_contig_like
Usage   : my @contig_like_objs = $csp->_get_contig_like($assembly_obj);
Function: Get contigs and singlets from an assembly, contig or singlet
Returns : array of Bio::Assembly::Contig and Singlet objects
Args    : a Bio::Assembly::Scaffold, Contig or singlet object

_get_assembly_seq_stats

Title   : _get_assembly_seq_stats
Usage   : my $seqlength = $csp->_get_assembly_seq_stats($assemblyobj);
Function: Get sequence statistics from an assembly:
            average sequence length, number of sequences
Returns : average sequence length (decimal)
          number of sequences (integer)
Args    : Bio::Assembly::Scaffold, Contig or singlet object
          hash reference with the IDs of the sequences to consider [optional]

_get_contig_seq_stats

Title   : _get_contig_seq_stats
Usage   : my $seqlength = $csp->_get_contig_seq_stats($contigobj);
Function: Get sequence statistics from a contig:
            average sequence length, number of sequences
Returns : average sequence length (decimal)
          number of sequences (integer)
Args    : contig object reference
          hash reference with the IDs of the sequences to consider [optional]

_update_seq_stats

Title   : _update_seq_stats
Usage   : 
Function: Update the number of sequences and their average length 1
          average identity 1
          minimum length 1
          minimum identity 1
          number of overlaps 1 average sequence length
Returns : average sequence length
          number of sequences
Args    : average sequence length 1
          number of sequences 1
          average sequence length 2
          number of sequences 2

_get_assembly_overlap_stats

Title   : _get_assembly_overlap_stats
Usage   : my ($avglength, $avgidentity, $minlength, $min_identity, $nof_overlaps)
            = $csp->_get_assembly_overlap_stats($assemblyobj);
Function: Get statistics about pairwise overlaps in contigs of an assembly
Returns : average overlap length
          average identity percent
          minimum overlap length
          minimum identity percent
          number of overlaps
Args    : Bio::Assembly::Scaffold, Contig or Singlet object
          hash reference with the IDs of the sequences to consider [optional]

_get_contig_overlap_stats

Title   : _get_contig_overlap_stats
Usage   : my ($avglength, $avgidentity, $minlength, $min_identity, $nof_overlaps)
            = $csp->_get_contig_overlap_stats($contigobj);
Function: Get statistics about pairwise overlaps in a contig or singlet. The
            statistics are obtained using graph theory: each read is a node
            and the edges between 2 reads are weighted by minus the number of
            conserved residues in the alignment between the 2 reads. The
            minimum spanning tree of this graph represents the overlaps that
            form the contig. Overlaps that do not satisfy the minimum overlap
            length and similarity get a malus on their score.
            Note: This function requires the optional BioPerl dependency
            module called 'Graph'
Returns : average overlap length
          average identity percent
          minimum overlap length
          minimum identity percent
          number of overlaps
Args    : Bio::Assembly::Contig or Singlet object
          hash reference with the IDs of the sequences to consider [optional]

_update_overlap_stats

Title   : _update_overlap_stats
Usage   : 
Function: update the number of overlaps and their minimum and average length
          and identity
Returns : 
Args    : average length 1
          average identity 1
          minimum length 1
          minimum identity 1
          number of overlaps 1
          average length 2
          average identity 2
          minimum length 2
          minimum identity 2
          number of overlaps 2

_overlap_alignment

Title   : _overlap_alignment
Usage   : 
Function: Produce an alignment of the overlapping section of two sequences of
          a contig. Minimum overlap length and percentage identity can be
          specified. Return undef if the sequences do not overlap or do not
          meet the minimum overlap criteria.
Return  : Bio::SimpleAlign object reference
          alignment overlap length
          alignment overlap identity
Args    : Bio::Assembly::Contig object reference
          Bio::LocatableSeq contig sequence 1
          Bio::LocatableSeq contig sequence 2
          minium overlap length [optional]
          minimum overlap identity percentage[optional]

_contig_graph

Title   : _contig_graph
Usage   : 
Function: Creates a graph data structure of the contig.The graph is undirected.
          The vertices are the reads of the contig and edges are the overlap
          between the reads. The edges are weighted by the opposite of the
          overlap, so it is negative and the better the overlap, the lower the
          weight.
Return  : Graph object or undef
          hashref of overlaps (score, length, identity) for each read pair
Args    : Bio::Assembly::Contig object reference
          hash reference with the IDs of the sequences to consider [optional]
          minimum overlap length (integer)                         [optional]
          minimum percentage identity (integer)                    [optional]

_draw_graph

Title   : _draw_graph
Usage   : 
Function: Generates a PNG picture of the contig graph. It is mostly for
          debugging purposes.
Return  : 1 for success
Args    : a Graph object
          hashref of overlaps (score, length, identity) for each read pair
          name of output file
          overlap info to display: 'score' (default), 'length' or 'identity'