Bio::Assembly::Tools::UseriContributed)Bio::Assembly::Tools::ContigSpectrum(3)NAMEBio::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: ".$from_assembly->avg_seq_length." bp\n";
print "Minimum overlap length: ".$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)
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_seq number of sequences
nof_rep number of repetitions (assemblies) used
max_size size of (number of sequences in) the largest contig
nof_overlaps number of overlaps
min_overlap minimum overlap length for building a contig
min_identity minimum sequence identity over the overlap length
avg_overlap average overlap length
avg_identity average overlap identity
avg_seq_length average sequence length
eff_asm_params effective assembly parameters
spectrum hash representation of a contig spectrum
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
dissolve calculate a dissolved contig spectrum (based on assembly)
cross produce a cross contig spectrum (based on assembly)
add add a contig spectrum to an existing one
average make an average of several contig spectra
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, ...
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
http://bugzilla.bioperl.org/
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 calulated. 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 @asm_list = $csp->assembly();
Function: Get a reference to the list of assembly object reference used to
make the contig spectrum object / Update the contig spectrum object
based on an assembly object.
Returns : array of Bio::Assembly::Scaffold
Args : Bio::Assembly::Scaffold
drop_assembly
Title : drop_assembly
Usage : $csp->drop_assembly();
Function: Remove all assembly objects associated with a contig spectrum.
Assembly objects can be big. This method allows to free some memory
when assembly information is not needed anymore.
Returns : 1 for success, 0 for failure
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 based on the assembly.
The mixed contig spectrum object must have been created based on one
(or several) assembly object(s). Additionally, min_overlap and
min_identity must have been set (either manually using min_overlap
or automatically by switching on the eff_asm_params option).
Returns : 1 for success, 0 for failure
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.
Returns : 1 for success, 0 for failure
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, 0 for failure
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
Args : number of total sequences to assume [optional]
_naive_assembler
Title : _naive_assembler
Usage :
Function: Determines the contig spectrum (hash representation) of a subset of
sequences from a mixed contig spectrum by "reassembling" 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. There is no actual alignment done
Returns : contig spectrum hash reference
Args : Bio::Assembly::Contig
sequence ID array reference
minimum overlap length (integer) [optional]
minimum percentage identity (integer) [optional]
_new_from_assembly
Title : _new_from_assembly
Usage :
Function: Creates a new contig spectrum object based solely on the result of
an assembly
Returns : Bio::Assembly::Tools::ContigSpectrum
Args : Bio::Assembly::Scaffold
_new_dissolved_csp
Title :
Usage : create a dissolved contig spectrum object
Function:
Returns :
Args :
_new_cross_csp
Title :
Usage :
Function: create a cross contig spectrum object
Returns :
Args :
_import_assembly
Title : _import_assembly
Usage : $csp->_import_assembly($assemblyobj);
Function: Update a contig spectrum object based on an assembly object
Returns : 1 for success, 0 for error
Args : Bio::Assembly::Scaffold assembly 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, 0 for error
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, 0 for error
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, 0 for error
Args : Bio::Assembly::Tools::ContigSpectrum
_get_seq_stats
Title : _get_seq_stats
Usage : my $seqlength = $csp->_get_seq_stats($assemblyobj);
Function: Get sequence statistics from an assembly:
number of sequences, average sequence length
Returns : number of sequences (integer)
average sequence length (decimal)
Args : assembly object reference
hash reference with the IDs of the sequences to consider [optional]
_get_overlap_stats
Title : _get_overlap_stats
Usage : my ($minlength, $min_identity, $avglength, $avgidentity)
= $csp->_get_overlap_stats($assemblyobj);
Function: Get statistics about pairwise overlaps in contigs of an assembly
Returns : number of overlaps
minimum overlap length
average overlap length
minimum identity percent
average identity percent
Args : assembly object reference
hash reference with the IDs of the sequences to consider [optional]
_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 percentage identity [optional]
perl v5.14.12011-Bio::Assembly::Tools::ContigSpectrum(3)
