Bio::Assembly::Tools
ContigSpectrum
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Summary
Bio::Assembly::Tools::ContigSpectrum - create and manipulate contig spectra
Package variables
No package variables defined.
Included modules
Inherit
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.
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.
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, ...
Methods
Methods description
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 |
Title : id
Usage : $csp->id
Function: get/set contig spectrum id
Returns : string
Args : string [optional] |
Title : nof_seq
Usage : $csp->nof_seq
Function: get/set the number of sequences making up the contig spectrum
Returns : integer
Args : integer [optional] |
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] |
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] |
Title : nof_overlaps
Usage : $csp->nof_overlaps
Function: Get/Set the number of overlaps in the assembly.
Returns : integer
Args : integer [optional] |
Title : min_overlap
Usage : $csp->min_overlap
Function: get/set the assembly minimum overlap length
Returns : integer
Args : integer [optional] |
Title : avg_overlap
Usage : $csp->avg_overlap
Function: get/set the assembly average overlap length
Returns : decimal
Args : decimal [optional] |
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] |
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] |
Title : avg_seq_len
Usage : $csp->avg_seq_len
Function: get/set the assembly average sequence length
Returns : avg_seq_len
Args : real [optional] |
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] |
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] |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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] |
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] |
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 |
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 |
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 |
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 |
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 |
Title : _new_cross_csp
Usage :
Function: create a cross contig spectrum object
Returns : cross-contig spectrum
Args : mixed contig spectrum |
Title : _cross_contig
Usage :
Function: calculate cross contigs
Returns : arrayref of cross-contigs
number of cross-singlets
Args : contig
minimum overlap
minimum identity |
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 |
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 |
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 |
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 |
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 |
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 |
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] |
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] |
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 |
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] |
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] |
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 |
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] |
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] |
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' |
Methods code
sub new
{ my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ( $id, $nof_seq, $nof_rep, $max_size, $nof_overlaps, $min_overlap,
$min_identity, $avg_overlap, $avg_identity, $avg_seq_len, $spectrum,
$assembly, $eff_asm_params, $dissolve, $cross) = $self->_rearrange(
[qw(ID NOF_SEQ NOF_REP MAX_SIZE NOF_OVERLAPS MIN_OVERLAP MIN_IDENTITY
AVG_OVERLAP AVG_IDENTITY AVG_SEQ_LEN SPECTRUM ASSEMBLY EFF_ASM_PARAMS
DISSOLVE CROSS)], @args );
$self->{'_id'} = 'NoName';
$self->{'_nof_seq'} = 0;
$self->{'_nof_rep'} = 0;
$self->{'_max_size'} = 0;
$self->{'_nof_overlaps'} = 0;
$self->{'_min_overlap'} = undef;
$self->{'_min_identity'} = undef;
$self->{'_avg_overlap'} = 0;
$self->{'_avg_identity'} = 0;
$self->{'_avg_seq_len'} = 0;
$self->{'_eff_asm_params'} = 0;
$self->{'_spectrum'} = {1 => 0};
$self->{'_assembly'} = [];
$self->{'_id'} = $id if (defined $id);
$self->{'_nof_seq'} = $nof_seq if (defined $nof_seq);
$self->{'_nof_rep'} = $nof_rep if (defined $nof_rep);
$self->{'_max_size'} = $max_size if (defined $max_size);
$self->{'_nof_overlaps'} = $nof_overlaps if (defined $nof_overlaps);
$self->{'_min_overlap'} = $min_overlap if (defined $min_overlap);
$self->{'_avg_overlap'} = $avg_overlap if (defined $avg_overlap);
$self->{'_min_identity'} = $min_identity if (defined $min_identity);
$self->{'_avg_identity'} = $avg_identity if (defined $avg_identity);
$self->{'_avg_seq_len'} = $avg_seq_len if (defined $avg_seq_len);
$self->{'_eff_asm_params'} = $eff_asm_params if (defined $eff_asm_params);
$self->_import_spectrum($spectrum) if defined($spectrum);
$self->_import_assembly($assembly) if defined($assembly);
$self->_import_cross_csp($cross) if defined($cross);
if (defined($dissolve)) {
my ($mixed_csp, $header) = (@$dissolve[0], @$dissolve[1]);
$self->_import_dissolved_csp($mixed_csp, $header);
}
return $self;} | sub id
{ my ($self, $id) = @_;
if (defined $id) {
$self->{'_id'} = $id;
}
$id = $self->{'_id'};
return $id;} | sub nof_seq
{ my ($self, $nof_seq) = @_;
if (defined $nof_seq) {
$self->throw("The number of sequences must be strictly positive. Got ".
"'$nof_seq'") if $nof_seq < 1;
$self->{'_nof_seq'} = $nof_seq;
}
$nof_seq = $self->{'_nof_seq'};
return $nof_seq;} | sub nof_rep
{ my ($self, $nof_rep) = @_;
if (defined $nof_rep) {
$self->throw("The number of repetitions must be strictly positive. Got ".
"'$nof_rep'") if $nof_rep < 1;
$self->{'_nof_rep'} = $nof_rep;
}
$nof_rep = $self->{'_nof_rep'};
return $nof_rep;} | sub max_size
{ my ($self, $max_size) = @_;
if (defined $max_size) {
$self->throw("The contig maximum size must be strictly positive. Got ".
"'$max_size'") if $max_size < 1;
$self->{'_max_size'} = $max_size;
}
$max_size = $self->{'_max_size'};
return $max_size;} | sub nof_overlaps
{ my ($self, $nof_overlaps) = @_;
if (defined $nof_overlaps) {
$self->throw("The number of overlaps must be strictly positive. Got ".
"'$nof_overlaps'") if $nof_overlaps < 1;
$self->{'_nof_overlaps'} = $nof_overlaps;
}
$nof_overlaps = $self->{'_nof_overlaps'};
return $nof_overlaps;} | sub min_overlap
{ my ($self, $min_overlap) = @_;
if (defined $min_overlap) {
$self->throw("The minimum of overlap length must be strictly positive. Got".
" '$min_overlap'") if $min_overlap < 1;
$self->{'_min_overlap'} = $min_overlap;
}
$min_overlap = $self->{'_min_overlap'};
return $min_overlap;} | sub avg_overlap
{ my ($self, $avg_overlap) = @_;
if (defined $avg_overlap) {
$self->throw("The average overlap length must be strictly positive. Got ".
"'$avg_overlap'") if $avg_overlap < 1;
$self->{'_avg_overlap'} = $avg_overlap;
}
$avg_overlap = $self->{'_avg_overlap'};
return $avg_overlap;} | sub min_identity
{ my ($self, $min_identity) = @_;
if (defined $min_identity) {
$self->throw("The minimum overlap percent identity must be strictly ".
"positive. Got '$min_identity'") if $min_identity < 1;
$self->{'_min_identity'} = $min_identity;
}
$min_identity = $self->{'_min_identity'};
return $min_identity;} | sub avg_identity
{ my ($self, $avg_identity) = @_;
if (defined $avg_identity) {
$self->throw("The average overlap percent identity must be strictly ".
"positive. Got '$avg_identity'") if $avg_identity < 1;
$self->{'_avg_identity'} = $avg_identity;
}
$avg_identity = $self->{'_avg_identity'};
return $avg_identity;} | sub avg_seq_len
{ my ($self, $avg_seq_len) = @_;
if (defined $avg_seq_len) {
$self->throw("The average sequence length must be strictly positive. Got ".
"'$avg_seq_len'") if $avg_seq_len < 1;
$self->{'_avg_seq_len'} = $avg_seq_len;
}
$avg_seq_len = $self->{'_avg_seq_len'};
return $avg_seq_len;} | sub eff_asm_params
{ my ($self, $eff_asm_params) = @_;
if (defined $eff_asm_params) {
$self->throw("eff_asm_params can only take values 0 or 1. Input value was ".
"'$eff_asm_params'") unless $eff_asm_params == 0 || $eff_asm_params == 1;
$self->{'_eff_asm_params'} = $eff_asm_params;
}
$eff_asm_params = $self->{'_eff_asm_params'};
return $eff_asm_params;} | sub spectrum
{ my ($self, $spectrum) = @_;
if (defined $spectrum) {
$self->_import_spectrum($spectrum);
}
$spectrum = $self->{'_spectrum'};
return $spectrum;} | sub assembly
{ my ($self, $assembly) = @_;
if (defined $assembly) {
$self->_import_assembly($assembly);
}
my @obj_list = @{$self->{'_assembly'}} if defined $self->{'_assembly'};
return @obj_list;} | sub drop_assembly
{ my ($self) = @_;
$self->{'_assembly'} = [];
return 1;} | sub dissolve
{ my ($self, $mixed_csp, $seq_header) = @_;
$self->_import_dissolved_csp($mixed_csp, $seq_header);
return 1; } | sub cross
{ my ($self, $mixed_csp) = @_;
$self->_import_cross_csp($mixed_csp);
return 1; } | sub to_string
{ my ($self, $element_separator) = @_;
return 0 if $self->{'_max_size'} == 0;
$element_separator ||= 1;
if ($element_separator == 1) {
$element_separator = ' ';
} elsif ($element_separator == 2) {
$element_separator = "\t";
} elsif ($element_separator == 3) {
$element_separator = "\n";
} else {
$self->throw("Unknown separator type '$element_separator'\n");
}
my $str = '';
for (my $q = 1 ; $q <= $self->{'_max_size'} ; $q++) {
my $val = 0;
if (exists $self->{'_spectrum'}{$q}) {
$val = $self->{'_spectrum'}{$q};
}
$str .= $val.$element_separator;
}
$str =~ s/\s$//;
return $str;} | sub add
{ my ($self, $csp) = @_;
if( !ref $csp || ! $csp->isa('Bio::Assembly::Tools::ContigSpectrum') ) {
$self->throw("Unable to process non Bio::Assembly::Tools::ContigSpectrum ".
"object [".ref($csp)."]");
}
if ( $self->{'_eff_asm_params'} > 0 ) {
if ( $csp->{'_eff_asm_params'} == 0 ) {
$self->warn("The parent contig spectrum needs effective assembly ".
"parameters (eff_asm_params = ".$self->{'_eff_asm_params'}.") but the ".
"child contig spectrum doesn't have them (eff_asm_params = ".
$csp->{'_eff_asm_params'}."). Skipping them...");
} elsif ( $csp->{'_eff_asm_params'} != $self->{'_eff_asm_params'} ) {
$self->warn("The parent contig spectrum needs a different method for ".
"detecting the effective assembly parameters (eff_asm_params = ".
$self->{'_eff_asm_params'}.") than the one specified for the child ".
"contig spectrum (eff_asm_params = ".$csp->{'_eff_asm_params'}."). ".
"Ignoring the differences...");
}
( $self->{'_avg_overlap'} , $self->{'_avg_identity'}, $self->{'_min_overlap'},
$self->{'_min_identity'}, $self->{'_nof_overlaps'} ) = $self->_update_overlap_stats(
$self->{'_avg_overlap'} , $self->{'_avg_identity'}, $self->{'_min_overlap'},
$self->{'_min_identity'}, $self->{'_nof_overlaps'},
$csp->{'_avg_overlap'} , $csp->{'_avg_identity'} , $csp->{'_min_overlap'},
$csp->{'_min_identity'} , $csp->{'_nof_overlaps'} );
}
( $self->{'_avg_seq_len'} ) = $self->_update_seq_stats(
$self->{'_avg_seq_len'}, $self->{'_nof_seq'}, $csp->{'_avg_seq_len'},
$csp->{'_nof_seq'} );
$self->_import_spectrum($csp->{'_spectrum'});
$self->{'_nof_rep'}--;
$self->{'_nof_rep'} += $csp->{'_nof_rep'};
push @{$self->{'_assembly'}}, @{$csp->{'_assembly'}}
if defined $csp->{'_assembly'};
return 1; } | sub average
{ my ($self, $list) = @_;
if ( ! ref $list || ! ref $list eq 'ARRAY') {
$self->throw("Average takes an array reference but got [".ref($list)."]");
}
my $avg = Bio::Assembly::Tools::ContigSpectrum->new;
$avg->{'_eff_asm_params'} = $self->{'_eff_asm_params'};
my $tot_nof_rep = 0;
for my $csp (@$list) {
if (not $csp->isa('Bio::Assembly::Tools::ContigSpectrum')) {
$csp->throw("Unable to process non Bio::Assembly::Tools::ContigSpectrum ".
"object [".ref($csp)."]");
}
$avg->add($csp);
}
for (my $q = 1 ; $q <= $avg->{'_max_size'} ; $q++) {
$avg->{'_spectrum'}{$q} /= $avg->{'_nof_rep'}
if (defined $avg->{'_spectrum'}{$q});
}
$avg->{'_nof_seq'} /= $avg->{'_nof_rep'};
$avg->{'_nof_overlaps'} /= $avg->{'_nof_rep'};
return $avg; } | sub score
{ my ($self, $nof_seqs) = @_;
my $n = $self->nof_seq;
return undef if ($n <= 0);
my $score = 0;
my $q_max = $self->max_size;
my $spec = $self->spectrum;
for my $q ( 1 .. $q_max ) {
my $c_q = $spec->{$q};
if ( $q == 1 && $nof_seqs ) {
$c_q += $nof_seqs - $n;
$n = $nof_seqs;
}
next if not $c_q;
$score += $c_q * $q ** 2;
}
$score /= $n ** 2;
$score = $n/($n-1) * ($score - 1/$n);
return $score; } | sub _naive_assembler
{ my ($self, $contig, $seqlist, $min_overlap, $min_identity) = @_;
if (not defined $seqlist) {
for my $seq ($contig->each_seq) {
push @$seqlist, $seq->id;
}
}
if ( ! ref $seqlist || ! ref($seqlist) eq 'ARRAY') {
$self->throw('Expecting an array reference. Got ['.ref($seqlist)."]\n ");
}
my $max = scalar @$seqlist;
$self->throw("Expecting at least 2 sequences as input for _naive_assembler")
if ($max < 2);
my %seq_hash = map { $_ => undef } (@$seqlist) if (scalar @$seqlist > 0);
my ($g, $overlaps) = $self->_contig_graph($contig,\% seq_hash, $min_overlap, $min_identity);
my @contig_objs;
my $num = 1;
if (defined $g) {
for my $connected_reads ($g->connected_components) {
my $sub_id = $contig->id.'_'.$num;
my $sub_contig = $self->_create_subcontig($contig, $connected_reads, $sub_id);
push @contig_objs, $sub_contig;
$num++;
for my $read_id ( @$connected_reads ) {
delete $seq_hash{$read_id};
}
}
}
my @singlet_objs;
for my $read_id ( keys %seq_hash ) {
my $read = $contig->get_seq_by_name($read_id);
my $sub_singlet = Bio::Assembly::Singlet->new(
-id => $contig->id.'_'.$num,
-seqref => $self->_obj_copy($read)
);
$num++;
push @singlet_objs, $sub_singlet;
}
return [@contig_objs, @singlet_objs]; } | sub _create_subcontig
{ my ($self, $contig, $read_ids, $sub_contig_id) = @_;
my $sub_contig = Bio::Assembly::Contig->new( -id => $sub_contig_id );
my ($min, $max) = (undef, undef);
for my $read_id ( @$read_ids ) {
my ($aln_coord) = $contig->get_features_collection->get_features_by_type("_aligned_coord:$read_id");
my $seq_start = $aln_coord->location->start;
my $seq_end = $aln_coord->location->end;
$min = $seq_start if (not defined $min) || ((defined $min) && ($seq_start < $min));
$max = $seq_end if (not defined $max) || ((defined $max) && ($seq_end > $max));
}
for my $read_id (@$read_ids) {
my $read = $self->_obj_copy($contig->get_seq_by_name($read_id));
my $coord = $self->_obj_copy($contig->get_seq_coord($read));
if ($min > 1) {
$coord->start( $coord->start - $min + 1 );
$coord->end( $coord->end - $min + 1 );
}
$sub_contig->set_seq_coord($coord, $read);
}
my $cons_seq = $contig->get_consensus_sequence;
$sub_contig->set_consensus_sequence( $self->_obj_copy($cons_seq, $min, $max) );
my $cons_qual = $contig->get_consensus_quality;
if ($cons_qual) {
$sub_contig->set_consensus_quality( $self->_obj_copy($cons_qual, $min, $max) );
}
return $sub_contig; } | sub _obj_copy
{ my ($self, $obj, $start, $end) = @_;
my $new;
if ($obj->isa('Bio::Seq::PrimaryQual')) {
my $qual = [@{$obj->qual}];
if (defined $start && defined $end && $start !=1 && $end != scalar(@$qual)) {
$qual = [ splice @$qual, $start - 1, $end - $start + 1 ];
}
$new = Bio::Seq::PrimaryQual->new(
-qual => $qual,
-id => $obj->id,
);
} elsif ($obj->isa('Bio::LocatableSeq')) {
my $seq = $obj->seq;
if (defined $start && defined $end && $start != 1 && $end != length($seq)) {
$seq = substr $seq, $start - 1, $end - $start + 1;
}
$new = Bio::LocatableSeq->new(
-seq => $seq,
-id => $obj->id,
-start => $obj->start,
-strand => $obj->strand,
-alphabet => $obj->alphabet,
);
} elsif ($obj->isa('Bio::SeqFeature::Generic')) {
$new = Bio::SeqFeature::Generic->new(
-start => $obj->start,
-end => $obj->end
);
}
return $new;} | sub _new_from_assembly
{
my ($self, $assemblyobj) = @_;
my $csp = Bio::Assembly::Tools::ContigSpectrum->new();
$csp->{'_id'} = $assemblyobj->id;
$csp->{'_eff_asm_params'} = $self->{'_eff_asm_params'};
$csp->{'_min_overlap'} = $self->{'_min_overlap'};
$csp->{'_min_identity'} = $self->{'_min_identity'};
if ( $csp->{'_eff_asm_params'} > 0 ) {
( $csp->{'_avg_overlap'}, $csp->{'_avg_identity'}, $csp->{'_min_overlap'},
$csp->{'_min_identity'}, $csp->{'_nof_overlaps'} )
= $csp->_get_assembly_overlap_stats($assemblyobj);
}
($csp->{'_avg_seq_len'}, $csp->{'_nof_seq'}) = $self->_get_assembly_seq_stats($assemblyobj);
for my $contigobj ( $self->_get_contig_like($assemblyobj) ) {
my $size = $contigobj->num_sequences;
if (defined $csp->{'_spectrum'}{$size}) {
$csp->{'_spectrum'}{$size}++;
} else {
$csp->{'_spectrum'}{$size} = 1;
}
$csp->{'_max_size'} = $size if $size > $csp->{'_max_size'};
}
push @{$csp->{'_assembly'}}, $assemblyobj;
$csp->{'_nof_rep'} = 1;
return $csp; } | sub _new_dissolved_csp
{ my ($self, $mixed_csp, $seq_header) = @_;
if ($mixed_csp->{'_nof_overlaps'} > 0) {
unless ( defined $self->{'_min_overlap'} ||
defined $mixed_csp->{'_min_overlap'} ) {
$self->throw("min_overlap must be defined in the dissolved contig spectrum".
" or mixed contig spectrum to dissolve a contig");
}
unless ( defined $self->{'_min_identity'} ||
defined $mixed_csp->{'_min_identity'} ) {
$self->throw("min_identity must be defined in the dissolved contig spectrum".
" or mixed contig spectrum");
}
}
if (!defined $mixed_csp->{'_assembly'} ||
scalar @{$mixed_csp->{'_assembly'}} < 1) {
$self->throw("The mixed contig spectrum must be based on at least one
assembly");
}
my $dissolved = Bio::Assembly::Tools::ContigSpectrum->new();
my ($eff_asm_params, $min_overlap, $min_identity);
if ($self->{'_eff_asm_params'}) {
$eff_asm_params = $self->{'_eff_asm_params'};
} else {
$eff_asm_params = $mixed_csp->{'_eff_asm_params'};
}
if ($self->{'_min_overlap'}) {
$min_overlap = $self->{'_min_overlap'};
} else {
$min_overlap = $mixed_csp->{'_min_overlap'};
}
if ($self->{'_min_identity'}) {
$min_identity = $self->{'_min_identity'};
} else {
$min_identity = $mixed_csp->{'_min_identity'};
}
($dissolved->{'_eff_asm_params'}, $dissolved->{'_min_overlap'},
$dissolved->{'_min_identity'}) = ($eff_asm_params, $min_overlap,
$min_identity);
for my $obj (@{$mixed_csp->{'_assembly'}}) {
for my $contig ( $self->_get_contig_like($obj) ) {
my $dissolved_objs = $self->_dissolve_contig( $contig, $seq_header,
$min_overlap, $min_identity );
for my $dissolved_obj (@$dissolved_objs) {
$dissolved->assembly($dissolved_obj);
$dissolved->{'_nof_rep'}--;
}
}
}
$dissolved->{'_nof_rep'} += $mixed_csp->{'_nof_rep'};
return $dissolved; } | sub _dissolve_contig
{ my ($self, $contig, $wanted_origin, $min_overlap, $min_identity) = @_;
my @seqs;
if ($contig->isa('Bio::Assembly::Singlet')) {
@seqs = $contig->seqref;
} elsif ($contig->isa('Bio::Assembly::Contig')) {
@seqs = $contig->each_seq;
}
my @contig_seqs;
for my $seq (@seqs) {
my $seq_id = $seq->id;
next unless $self->_seq_origin($seq_id) eq $wanted_origin;
push @contig_seqs, $seq_id;
}
my $size = scalar @contig_seqs;
my $objs;
if ($size == 1) {
my $id = $contig_seqs[0];
my $seq = $contig->get_seq_by_name($id);
push @$objs, Bio::Assembly::Singlet->new(-id => $contig->id, -seqref => $self->_obj_copy($seq) );
} elsif ($size > 1) {
my $contig_objs = $self->_naive_assembler( $contig,\@ contig_seqs,
$min_overlap, $min_identity );
push @$objs, @$contig_objs;
}
return $objs; } | sub _new_cross_csp
{ my ($self, $mixed_csp) = @_;
if (!defined $mixed_csp->{'_assembly'} ||
scalar @{$mixed_csp->{'_assembly'}} < 1) {
$self->throw("The mixed contig spectrum must be based on at least one ".
"assembly.");
}
my $cross = Bio::Assembly::Tools::ContigSpectrum->new();
my ($eff_asm_params, $min_overlap, $min_identity);
if ($self->{'_eff_asm_params'}) {
$eff_asm_params = $self->{'_eff_asm_params'};
} else {
$eff_asm_params = $mixed_csp->{'_eff_asm_params'};
}
if ($self->{'_min_overlap'}) {
$min_overlap = $self->{'_min_overlap'};
} else {
$min_overlap = $mixed_csp->{'_min_overlap'};
}
if ($self->{'_min_identity'}) {
$min_identity = $self->{'_min_identity'};
} else {
$min_identity = $mixed_csp->{'_min_identity'};
}
($cross->{'_eff_asm_params'},$cross->{'_min_overlap'},$cross->{'_min_identity'})
= ($eff_asm_params, $min_overlap, $min_identity);
for my $obj ( @{$mixed_csp->{'_assembly'}} ) {
for my $contig ( $self->_get_contig_like($obj) ) {
my ($cross_contigs, $nof_cross_singlets) = $self->_cross_contig($contig,
$min_overlap, $min_identity);
for my $cross_contig ( @$cross_contigs ) {
$cross->assembly($cross_contig);
$cross->{'_nof_rep'}--;
}
$cross->{'_spectrum'}->{'1'} += $nof_cross_singlets;
}
}
$cross->{'_nof_rep'} += $mixed_csp->{'_nof_rep'};
return $cross; } | sub _cross_contig
{ my ($self, $contig, $min_overlap, $min_identity) = @_;
my $nof_cross_singlets = 0;
my @cross_contigs;
my %all_origins;
for my $seq ($contig->each_seq) {
my $seq_id = $seq->id;
my $seq_origin = $self->_seq_origin($seq_id);
if (not defined $seq_origin) {
$self->warn("Sequence $seq_id doesn't have any header. Skipping it...");
next;
}
if ( scalar keys %all_origins > 1 ) {
last;
}
$all_origins{$seq_origin} = undef;
}
if ( scalar keys %all_origins <= 1 ) {
return\@ cross_contigs, $nof_cross_singlets;
}
%all_origins = ();
my $test_contigs = $self->_naive_assembler($contig, undef, $min_overlap, $min_identity);
for my $test_contig ( @$test_contigs ) {
my %origins;
for my $seq ($test_contig->each_seq) {
my $seq_id = $seq->id;
my $seq_origin = $self->_seq_origin($seq_id);
next if not defined $seq_origin;
push @{$origins{$seq_origin}}, $seq_id;
}
if (scalar keys %origins > 1) {
push @cross_contigs, $test_contig;
} else {
next;
}
for my $origin (keys %origins) {
my @ori_ids = @{$origins{$origin}};
if (scalar @ori_ids == 1) {
$nof_cross_singlets++;
} elsif (scalar @ori_ids > 1) {
my $ori_contigs = $self->_naive_assembler($test_contig,\@ ori_ids, undef, undef);
for my $ori_contig (@$ori_contigs) {
$nof_cross_singlets++ if $ori_contig->num_sequences == 1;
}
}
}
}
return\@ cross_contigs, $nof_cross_singlets; } | sub _seq_origin
{
my ($self, $seq_id) = @_;
my $origin;
if ( $seq_id =~ m/^(.+?)\|/ ) {
$origin = $1;
}
return $origin; } | sub _import_assembly
{ my ($self, $assemblyobj) = @_;
if ( ! ref $assemblyobj ||
( ! $assemblyobj->isa('Bio::Assembly::ScaffoldI') &&
! $assemblyobj->isa('Bio::Assembly::Contig') )) {
$self->throw("Unable to process non Bio::Assembly::ScaffoldI, Contig or ".
"Singlet object [".ref($assemblyobj)."]");
}
my $csp = $self->_new_from_assembly($assemblyobj);
$self->add($csp);
return 1; } | sub _import_spectrum
{ my ($self, $spectrum) = @_;
if( ! ref $spectrum || ! ref $spectrum eq 'HASH') {
$self->throw("Spectrum should be a hash reference, but it is [".
ref($spectrum)."]");
}
for my $size (keys %$spectrum) {
if (defined $self->{'_spectrum'}{$size}) {
$self->{'_spectrum'}{$size} += $$spectrum{$size};
} else {
$self->{'_spectrum'}{$size} = $$spectrum{$size};
}
$self->{'_nof_seq'} += $size * $$spectrum{$size};
$self->{'_max_size'} = $size if $size > $self->{'_max_size'};
}
$self->{'_max_size'} = 0 if scalar keys %{$self->{'_spectrum'}} == 1 &&
defined $self->{'_spectrum'}{'1'} && $self->{'_spectrum'}{'1'} == 0;
$self->{'_nof_rep'}++;
return 1; } | sub _import_dissolved_csp
{ my ($self, $mixed_csp, $seq_header) = @_;
if (not defined $mixed_csp || not defined $seq_header) {
$self->throw("Expecting a contig spectrum reference and sequence header as".
" arguments");
}
my $dissolved_csp = $self->_new_dissolved_csp($mixed_csp, $seq_header);
$self->add($dissolved_csp);
return 1; } | sub _import_cross_csp
{ my ($self, $mixed_csp) = @_;
if (not defined $mixed_csp) {
$self->throw("Expecting a contig spectrum reference as argument");
}
my $cross_csp = $self->_new_cross_csp($mixed_csp);
my $nof_1_cross_contigs = $cross_csp->spectrum->{1};
$self->add($cross_csp);
$self->{'_nof_seq'} -= $nof_1_cross_contigs;
return 1; } | sub _get_contig_like
{ my ($self, $assembly_obj) = @_;
my @contig_objs;
if ($assembly_obj->isa('Bio::Assembly::ScaffoldI')) {
push @contig_objs, ($assembly_obj->all_contigs, $assembly_obj->all_singlets);
} else {
@contig_objs = $assembly_obj;
}
return @contig_objs;} | sub _get_assembly_seq_stats
{ my ($self, $assemblyobj, $seq_hash) = @_;
if ( !defined $assemblyobj ||
( !$assemblyobj->isa('Bio::Assembly::ScaffoldI') &&
!$assemblyobj->isa('Bio::Assembly::Contig') ) ) {
$self->throw("Must provide a Bio::Assembly::Scaffold, Contig or Singlet object");
}
$self->throw("Expecting a hash reference. Got [".ref($seq_hash)."]")
if (defined $seq_hash && ! ref($seq_hash) eq 'HASH');
my @asm_stats = (0,0);
for my $contigobj ( $self->_get_contig_like($assemblyobj) ) {
@asm_stats = $self->_update_seq_stats( @asm_stats,
$self->_get_contig_seq_stats($contigobj, $seq_hash) );
}
return @asm_stats; } | sub _get_contig_seq_stats
{ my ($self, $contigobj, $seq_hash) = @_;
my @contig_stats = (0, 0);
for my $seqobj ($contigobj->each_seq) {
next if defined $seq_hash && !defined $$seq_hash{$seqobj->id};
my $seq_string;
if ($contigobj->isa('Bio::Assembly::Singlet')) {
$seq_string = $contigobj->seqref->seq;
} else {
$seq_string = $seqobj->seq;
}
my $seq_len = $seqobj->_ungapped_len;
my @seq_stats = ($seq_len);
@contig_stats = $self->_update_seq_stats(@contig_stats, @seq_stats);
}
return @contig_stats; } | sub _update_seq_stats
{ my ($self, $p_avg_length, $p_nof_seq, $n_avg_length, $n_nof_seq) = @_;
if (not defined $n_nof_seq) {
$n_nof_seq = 1;
}
my $avg_length = 0;
my $nof_seq = $p_nof_seq + $n_nof_seq;
if ($nof_seq != 0) {
$avg_length = ($p_avg_length * $p_nof_seq + $n_avg_length * $n_nof_seq) / $nof_seq;
}
return $avg_length, $nof_seq; } | sub _get_assembly_overlap_stats
{ my ($self, $assembly_obj, $seq_hash) = @_;
if ( !defined $assembly_obj ||
( !$assembly_obj->isa('Bio::Assembly::ScaffoldI') &&
!$assembly_obj->isa('Bio::Assembly::Contig') ) ) {
$self->throw("Must provide a Bio::Assembly::ScaffoldI, Contig or Singlet object");
}
$self->throw("Expecting a hash reference. Got [".ref($seq_hash)."]")
if (defined $seq_hash && ! ref($seq_hash) eq 'HASH');
my @asm_stats = (0, 0, undef, undef, 0);
for my $contig_obj ( $self->_get_contig_like($assembly_obj) ) {
@asm_stats = $self->_update_overlap_stats( @asm_stats,
$self->_get_contig_overlap_stats($contig_obj, $seq_hash) );
}
return @asm_stats; } | sub _get_contig_overlap_stats
{ my ($self, $contig_obj, $seq_hash) = @_;
$self->throw("Must provide a Bio::Assembly::Contig object")
if (!defined $contig_obj || !$contig_obj->isa("Bio::Assembly::Contig"));
$self->throw("Expecting a hash reference. Got [".ref($seq_hash)."]")
if (defined $seq_hash && ! ref($seq_hash) eq 'HASH');
my @contig_stats = (0, 0, undef, undef, 0);
my ($g, $overlaps) = $self->_contig_graph($contig_obj, $seq_hash);
if ( defined $g ) {
$g = $g->MST_Kruskal();
for my $edge ( $g->edges ) {
my ($id1, $id2) = @$edge;
if (not exists $$overlaps{$id1}{$id2}) {
($id2, $id1) = @$edge;
}
my ($score, $length, $identity) = @{$$overlaps{$id1}{$id2}};
my @overlap_stats = ($length, $identity);
@contig_stats = $self->_update_overlap_stats(@contig_stats, @overlap_stats);
}
}
return @contig_stats; } | sub _update_overlap_stats
{ my ($self,
$p_avg_length, $p_avg_identity, $p_min_length, $p_min_identity, $p_nof_overlaps,
$n_avg_length, $n_avg_identity, $n_min_length, $n_min_identity, $n_nof_overlaps)
= @_;
if (not defined $n_nof_overlaps) { $n_nof_overlaps = 1 };
if ((not defined $n_min_length) && ($n_avg_length != 0)) { $n_min_length = $n_avg_length };
if ((not defined $n_min_identity) && ($n_avg_identity != 0)) { $n_min_identity = $n_avg_identity };
my ($avg_length, $avg_identity, $min_length, $min_identity, $nof_overlaps)
= (0, 0, undef, undef, 0);
$nof_overlaps = $p_nof_overlaps + $n_nof_overlaps;
if ($nof_overlaps > 0) {
$avg_length = ($p_avg_length * $p_nof_overlaps + $n_avg_length * $n_nof_overlaps) / $nof_overlaps;
$avg_identity = ($p_avg_identity * $p_nof_overlaps + $n_avg_identity * $n_nof_overlaps) / $nof_overlaps;
}
if ( not defined $p_min_length ) {
$min_length = $n_min_length;
} elsif ( not defined $n_min_length ) {
$min_length = $p_min_length;
} else {
if ($n_min_length < $p_min_length) {
$min_length = $n_min_length;
} else {
$min_length = $p_min_length;
}
}
if ( not defined $p_min_identity ) {
$min_identity = $n_min_identity;
} elsif ( not defined $n_min_identity ) {
$min_identity = $p_min_identity;
} else {
if ($n_min_identity < $p_min_identity) {
$min_identity = $n_min_identity;
} else {
$min_identity = $p_min_identity;
}
}
return $avg_length, $avg_identity, $min_length, $min_identity, $nof_overlaps;} | sub _overlap_alignment
{ my ($self, $contig, $qseq, $tseq, $min_overlap, $min_identity) = @_;
my $qpos = $contig->get_seq_coord($qseq);
my $tpos = $contig->get_seq_coord($tseq);
my $qend = $qpos->end;
my $tstart = $tpos->start;
return if $qend < $tstart;
my $qstart = $qpos->start;
my $tend = $tpos->end;
return if $qstart > $tend;
my $left;
if ($qstart >= $tstart) {
$left = $qstart
} else {
$left = $tstart;
}
my $right;
if ($qend > $tend) {
$right = $tend;
} else {
$right = $qend;
}
my $overlap = $right - $left + 1;
return if defined $min_overlap && $overlap < $min_overlap;
my $qleft =
$contig->change_coord('gapped consensus', "aligned ".$qseq->id, $left);
my $qstring = substr($qseq->seq, $qleft - 1, $overlap);
my $tleft =
$contig->change_coord('gapped consensus', "aligned ".$tseq->id, $left);
my $tstring = substr($tseq->seq, $tleft - 1, $overlap);
for (my $pos = 0 ; $pos < $overlap ; $pos++) {
my $qnt = substr($qstring, $pos, 1);
if ($qnt eq '-') {
my $tnt = substr($tstring, $pos, 1);
if ($tnt eq '-') {
substr($qstring, $pos, 1, '');
substr($tstring, $pos, 1, '');
$pos--;
$overlap--;
}
}
}
return if defined $min_overlap && $overlap < $min_overlap;
my $qgaps = ($qstring =~ tr/-//);
my $tgaps = ($tstring =~ tr/-//);
my $aln = Bio::SimpleAlign->new;
my $alseq = Bio::LocatableSeq->new(
-id => 1,
-seq => $qstring,
-start => 1,
-end => $overlap - $qgaps,
-alphabet => 'dna',
);
$aln->add_seq($alseq);
$alseq = Bio::LocatableSeq->new(
-id => 2,
-seq => $tstring,
-start => 1,
-end => $overlap - $tgaps,
-alphabet => 'dna',
);
$aln->add_seq($alseq);
my $identity = $aln->overall_percentage_identity;
return if defined $min_identity && $identity < $min_identity;
return $aln, $overlap, $identity; } | sub _contig_graph
{ my ($self, $contig_obj, $seq_hash, $min_overlap, $min_identity) = @_;
if( !ref $contig_obj || ! $contig_obj->isa('Bio::Assembly::Contig') ) {
$self->throw("Unable to process non Bio::Assembly::Contig ".
"object [".ref($contig_obj)."]");
}
if (not eval { require Graph::Undirected }) {
$self->throw("Error: the module 'Graph' is needed by the method ".
"_contig_graph but could not be found\n$@");
}
my @seq_objs = $contig_obj->each_seq;
my $nof_seqs = scalar @seq_objs;
return if ($nof_seqs <= 1);
my %overlaps;
for my $i (0 .. $nof_seqs-1) {
my $seq_obj = $seq_objs[$i];
my $seq_id = $seq_obj->id;
next if defined $seq_hash && !exists $$seq_hash{$seq_id};
my ($best_score, $best_length, $best_identity);
for my $j ($i+1 .. $nof_seqs-1) {
my $target_obj = $seq_objs[$j];
my $target_id = $target_obj->id;
next if defined $seq_hash && !exists $$seq_hash{$target_id};
my ($aln_obj, $length, $identity)
= $self->_overlap_alignment($contig_obj, $seq_obj, $target_obj, $min_overlap, $min_identity);
next if ! defined $aln_obj;
my $score = $length * $identity / 100;
if ( ( $min_overlap && ($length < $min_overlap ) ) ||
( $min_identity && ($identity < $min_identity) ) ) {
$score = sqrt($score);
}
$overlaps{$seq_id}{$target_id} = [$score, $length, $identity];
}
}
my $g;
if (scalar keys %overlaps >= 1) {
$g = Graph::Undirected->new();
for my $seq_id (keys %overlaps) {
for my $target_id (keys %{$overlaps{$seq_id}}) {
my $score = @{$overlaps{$seq_id}{$target_id}}[0];
my $weight = -$score;
$g->add_weighted_edge($seq_id, $target_id, $weight);
}
}
}
return $g,\% overlaps; } | sub _draw_graph
{ my ($self, $g, $overlaps, $outfile, $edge_type) = @_;
$self->throw("Error: need to provide a graph as input\n") if not defined $g;
if (not eval { require GraphViz }) {
$self->throw("Error: the module 'GraphViz' is needed by the method ".
"_draw_graph but could not be found\n$@");
}
$edge_type ||= 'score';
my $viz = GraphViz->new( directed => 0 );
for my $edge ( $g->edges ) {
my ($id1, $id2) = @$edge;
if (not exists $$overlaps{$id1}{$id2}) {
($id2, $id1) = @$edge;
}
my ($score, $length, $identity) = @{$$overlaps{$id1}{$id2}};
my $edge_val;
if ($edge_type eq 'score') {
$edge_val = $score;
} elsif ($edge_type eq 'length') {
$edge_val = $length;
} elsif ($edge_type eq 'identity') {
$edge_val = $identity;
} else {
$self->throw("Error: invalid edge type to display, '$edge_val'");
}
$viz->add_edge($id1 => $id2, label => $edge_val);
}
open my $fh, '>', $outfile or die "Error: Could not write file '$outfile'\n$!\n";
print $fh $viz->as_png;
close $fh;
return 1;
}
1;
__END__} | General documentation
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
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.
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://redmine.open-bio.org/projects/bioperl/
| AUTHOR - Florent E Angly | Top |
Email florent_dot_angly_at_gmail_dot_com
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".