Bio::Assembly::Tools::ContigSpectrum
# 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";
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_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, ...
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".
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 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]
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 @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
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
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
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
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, 0 for failure 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 : _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]
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
Title : Usage : create a dissolved contig spectrum object Function: Returns : Args :
Title : Usage : Function: create a cross contig spectrum object Returns : Args :
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
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
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
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
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]
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]
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]
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.