Bio::Assembly::Contig.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Assembly::Contig - Perl module to hold and manipulate
                     sequence assembly contigs.

SYNOPSIS

     # Module loading
     use Bio::Assembly::IO;
 
     # Assembly loading methods
     $aio = Bio::Assembly::IO->new(-file=>"test.ace.1",
                                -format=>'phrap');
 
     $assembly = $aio->next_assembly;
     foreach $contig ($assembly->all_contigs) {
       # do something
     }
 
     # OR, if you want to build the contig yourself,
 
     use Bio::Assembly::Contig;
     $c = Bio::Assembly::Contig->new(-id=>"1");
 
     $ls  = Bio::LocatableSeq->new(-seq=>"ACCG-T",
                                   -id=>"r1",
                                   -alphabet=>'dna');
     $ls2 = Bio::LocatableSeq->new(-seq=>"ACA-CG-T",
                                   -id=>"r2",
                                   -alphabet=>'dna');
 
     $ls_coord = Bio::SeqFeature::Generic->new(-start=>3,
                                               -end=>8,
                                               -strand=>1);
     $ls2_coord = Bio::SeqFeature::Generic->new(-start=>1,
                                                -end=>8,
                                                -strand=>1);
     $c->add_seq($ls);
     $c->add_seq($ls2);
     $c->set_seq_coord($ls_coord,$ls);
     $c->set_seq_coord($ls2_coord,$ls2);
 
     $con = Bio::LocatableSeq->new(-seq=>"ACACCG-T",
                                   -alphabet=>'dna');
     $c->set_consensus_sequence($con);
 
     $l = $c->change_coord('unaligned r2','ungapped consensus',6);
     print "6 in unaligned r2 => $l in ungapped consensus\n";
 
 

DESCRIPTION

A contig is as a set of sequences, locally aligned to each other, so that every sequence has overlapping regions with at least one sequence in the contig, such that a continuous of overlapping sequences is formed, allowing the deduction of a consensus sequence which may be longer than any of the sequences from which it was deduced.

In this documentation we refer to the overlapping sequences used to build the contig as ``aligned sequences'' and to the sequence deduced from the overlap of aligned sequences as the ``consensus''. Methods to deduce the consensus sequence from aligned sequences were not yet implemented in this module, but its posssible to add a consensus sequence deduced by other means, e.g, by the assembly program used to build the alignment.

All aligned sequences in a Bio::Assembly::Contig must be Bio::Assembly::Locatable objects and have a unique ID. The unique ID restriction is due to the nature of the module's internal data structures and is also a request of some assembly programs. If two sequences with the same ID are added to a contig, the first sequence added is replaced by the second one.

Coordinate_systems

There are four base coordinate systems in Bio::Assembly::Contig. When you need to access contig elements or data that exists on a certain range or location, you may be specifying coordinates in relation to different sequences, which may be either the contig consensus or one of the aligned sequences that were used to do the assembly.
  =========================================================
           Name           | Referenced sequence
  ---------------------------------------------------------
    "gapped consensus"    | Contig (with gaps)
    "ungapped consensus"  | Contig (without gaps)
    "aligned $seqID"      | sequence $seqID (with gaps)
    "unaligned $seqID"    | sequence $seqID (without gaps)
  =========================================================
 
 

``gapped consensus'' refers to positions in the aligned consensus sequence, which is the consensus sequence including the gaps inserted to align it agains the aligned sequences that were used to assemble the contig. So, its limits are [ 1, (consensus length + number of gaps in consensus) ]

``ungapped consensus'' is a coordinate system based on the consensus sequence, but excluding consensus gaps. This is just the coordinate system that you have when considering the consensus sequence alone, instead of aligned to other sequences.

``aligned $seqID'' refers to locations in the sequence $seqID after alignment of $seqID against the consensus sequence (reverse complementing the original sequence, if needed). Coordinate 1 in ``aligned $seqID'' is equivalent to the start location (first base) of $seqID in the consensus sequence, just like if the aligned sequence $seqID was a feature of the consensus sequence.

``unaligned $seqID'' is equivalent to a location in the isolated sequence, just like you would have when considering the sequence alone, out of an alignment. When changing coordinates from ``aligned $seq2'' to ``unaligned $seq2'', if $seq2 was reverse complemented when included in the alignment, the output coordinates will be reversed to fit that fact, i.e. 1 will be changed to length($seq2), 2 will be length($seq)-1 and so on.

An important note: when you change gap coordinates from a gapped system (``gapped consensus'' or ``aligned $seqID'') to a system that does not include gaps (``ungapped consensus'' or ``unaligned $seqID''), the position returned will be the first location before all gaps neighboring the input location.

Feature_collection

Bio::Assembly::Contig stores much information about a contig in a Bio::Assembly::SeqFeature::Collection object. Relevant information on the alignment is accessed by selecting features based on their primary tags (e.g. all features which have a primary tag of the form '_aligned_coord:$seqID', where $seqID is an aligned sequence ID, are coordinates for sequences in the contig alignment) and, by using methods from Bio::Assembly::SeqFeature::Collection, it's possible to select features by overlap with other features.

We suggest that you use the primary tags of features as identifiers for feature classes. By convention, features with primary tags starting with a '_' are generated by modules that populate the contig data structure and return the contig object, maybe as part of an assembly object, e.g. drivers from the Bio::Assembly::IO set.

Features in the features collection may be associated with particular aligned sequences. To obtain this, you must attach the sequence to the feature, using attach() seq from Bio::Assembly::SeqFeatureI, before you add the feature to the feature collection. We also suggest to add the sequence id to the primary tag, so that is easy to select feature for a particular sequence.

There is only one feature class that some methods in Bio::Assembly::Contig expect to find in the feature collection: features with primary tags of the form '_aligned_coord:$seqID', where $seqID is the aligned sequence id (like returned by $seq->id()). These features describe the position (in ``gapped consensus'' coordinates) of aligned sequences, and the method set_seq_coord() automatically changes a feature's primary tag to this form whenever the feature is added to the collection by this method. Only two methods in Bio::Assembly::Contig will not work unless there are features from this class: change_coord() and get_seq_coord().

Other feature classes will be automatically available only when Bio::Assembly::Contig objects are created by a specific module. Such feature classes are (or should be) documented in the documentation of the module which create them, to which the user should refer.

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 the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Robson Francisco de Souza

rfsouza@citri.iq.usp.br

APPENDIX

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

Object creator

new

  Title     : new
  Usage     : my $contig = Bio::Assembly::Contig->new();
  Function  : Creates a new contig object
  Returns   : Bio::Assembly::Contig
  Args      : -id => contig unique ID
              -source => string for the sequence assembly program used
              -collection => Bio::SeqFeature::Collection instance
 
 
These methods exist to enable adding information about possible relations among contigs, e.g. when you already have a scaffold for your assembly, describing the ordering of contigs in the final assembly, but no sequences covering the gaps between neighboring contigs.

source

  Title     : source
  Usage     : $contig->source($program);
  Function  : Get/Set program used to build this contig
  Returns   : string
  Argument  : [optional] string
 
 

assembly

  Title     : assembly
  Usage     : $contig->assembly($assembly);
  Function  : Get/Set assembly object for this contig
  Returns   : a Bio::Assembly::Scaffold object
  Argument  : a Bio::Assembly::Scaffold object
 
 

strand

  Title     : strand
  Usage     : $contig->strand($num);
  Function  : Get/Set contig orientation in a scaffold/assembly.
              Its equivalent to the strand property of sequence
              objects and sets whether the contig consensus should
              be reversed and complemented before being added to a
              scaffold or assembly.
  Returns   : integer
  Argument  : 1 if orientaion is forward, -1 if reverse and
              0 if none
 
 

upstream_neighbor

  Title     : upstream_neighbor
  Usage     : $contig->upstream_neighbor($contig);
  Function  : Get/Set a contig neighbor for the current contig when
              building a scaffold. The upstream neighbor is
              located before $contig first base
  Returns   : nothing
  Argument  : Bio::Assembly::Contig
 
 

downstream_neighbor

  Title     : downstream_neighbor
  Usage     : $contig->downstream_neighbor($num);
  Function  : Get/Set a contig neighbor for the current contig when
              building a scaffold. The downstream neighbor is
              located after $contig last base
  Returns   : nothing
  Argument  : Bio::Assembly::Contig
 
 

Contig feature collection methods

add_features

  Title     : add_features
  Usage     : $contig->add_features($feat,$flag)
  Function  :
 
              Add an array of features to the contig feature
              collection. The consensus sequence may be attached to the
              added feature, if $flag is set to 1. If $flag is 0 and
              the feature attached to one of the contig aligned
              sequences, the feature is registered as an aligned
              sequence feature. If $flag is 0 and the feature is not
              attched to any sequence in the contig, the feature is
              simply added to the feature collection and no attachment
              or registration is made.
 
              Note: You must attach aligned sequences to their features
              prior to calling add_features, otherwise you won't be
              able to access the feature through get_seq_feat_by_tag()
              method.
 
  Returns   : number of features added.
  Argument  :
              $feat : A reference to an array of Bio::SeqFeatureI
              $flag : boolean - true if consensus sequence object
                      should be attached to this feature, false if
                      no consensus attachment should be made.
                      Default: false.
 
 

remove_features

  Title     : remove_features
  Usage     : $contig->remove_features(@feat)
  Function  : Remove an array of contig features
  Returns   : number of features removed.
  Argument  : An array of Bio::SeqFeatureI
 
 

get_features_collection

  Title     : get_features_collection
  Usage     : $contig->get_features_collection()
  Function  : Get the collection of all contig features
  Returns   : Bio::SeqFeature::Collection
  Argument  : none
 
 

remove_features_collection

  Title     : remove_features_collection
  Usage     : $contig->remove_features_collection()
  Function  : Remove the collection of all contig features. It is useful
              to save some memory (when contig features are not needed).
  Returns   : none
  Argument  : none
 
 
See Coordinate_Systems above.

change_coord

  Title     : change_coord
  Usage     : $contig->change_coord($in,$out,$query)
  Function  :
 
              Change coordinate system for $query.  This method
              transforms locations between coordinate systems described
              in section "Coordinate Systems" of this document.
 
              Note: this method will throw an exception when changing
              coordinates between "ungapped consensus" and other
              systems if consensus sequence was not set. It will also
              throw exceptions when changing coordinates among aligned
              sequence, either with or without gaps, and other systems
              if sequence locations were not set with set_seq_coord().
 
  Returns   : integer
  Argument  :
              $in    : [string]  input coordinate system
              $out   : [string]  output coordinate system
              $query : [integer] a position in a sequence
 
 

get_seq_coord

  Title     : get_seq_coord
  Usage     : $contig->get_seq_coord($seq);
  Function  : Get "gapped consensus" location for aligned sequence
  Returns   : Bio::SeqFeature::Generic for coordinates or undef.
              A warning is printed if sequence coordinates were not set.
  Argument  : Bio::LocatabaleSeq object
 
 

set_seq_coord

  Title     : set_seq_coord
  Usage     : $contig->set_seq_coord($feat,$seq);
  Function  :
 
              Set "gapped consensus" location for an aligned
              sequence. If the sequence was previously added using
              add_seq, its coordinates are changed/set.  Otherwise,
              add_seq is called and the sequence is added to the
              contig.
 
  Returns   : Bio::SeqFeature::Generic for old coordinates or undef.
  Argument  :
              $feat  : a Bio::SeqFeature::Generic object
                       representing a location for the
                       aligned sequence, in "gapped
                       consensus" coordinates.
 
              Note: the original feature primary tag will
                    be lost.
 
              $seq   : a Bio::LocatabaleSeq object
 
 

Bio::Assembly::Contig consensus methods

set_consensus_sequence

  Title     : set_consensus_sequence
  Usage     : $contig->set_consensus_sequence($seq)
  Function  : Set the consensus sequence object for this contig
  Returns   : consensus length
  Argument  : Bio::LocatableSeq
 
 

set_consensus_quality

  Title     : set_consensus_quality
  Usage     : $contig->set_consensus_quality($qual)
  Function  : Set the quality object for consensus sequence
  Returns   : nothing
  Argument  : Bio::Seq::QualI object
 
 

get_consensus_length

  Title     : get_consensus_length
  Usage     : $contig->get_consensus_length()
  Function  : Get consensus sequence length
  Returns   : integer
  Argument  : none
 
 

get_consensus_sequence

  Title     : get_consensus_sequence
  Usage     : $contig->get_consensus_sequence()
  Function  : Get a reference to the consensus sequence object
              for this contig
  Returns   : Bio::SeqI object
  Argument  : none
 
 

get_consensus_quality

  Title     : get_consensus_quality
  Usage     : $contig->get_consensus_quality()
  Function  : Get a reference to the consensus quality object
              for this contig.
  Returns   : A Bio::QualI object
  Argument  : none
 
 

Bio::Assembly::Contig aligned sequences methods

set_seq_qual

  Title     : set_seq_qual
  Usage     : $contig->set_seq_qual($seq,$qual);
  Function  : Adds quality to an aligned sequence.
  Returns   : nothing
  Argument  : a Bio::LocatableSeq object and
              a Bio::Seq::QualI object
 
 

See Bio::LocatableSeq for more information.

get_seq_ids

  Title     : get_seq_ids
  Usage     : $contig->get_seq_ids(-start=>$start,
                   -end=>$end,
                   -type=>"gapped A0QR67B08.b");
  Function  : Get list of sequence IDs overlapping interval [$start, $end]
              The default interval is [1,$contig->length]
              Default coordinate system is "gapped contig"
  Returns   : An array
  Argument  : A hash with optional elements:
              -start : consensus subsequence start
              -end   : consensus subsequence end
              -type  : the coordinate system type for $start and $end arguments
                       Coordinate system avaliable are:
                       "gapped consensus"   : consensus coordinates with gaps
                       "ungapped consensus" : consensus coordinates without gaps
                       "aligned $ReadID"    : read $ReadID coordinates with gaps
                       "unaligned $ReadID"  : read $ReadID coordinates without gaps
 
 

get_seq_feat_by_tag

  Title     : get_seq_feat_by_tag
  Usage     : $seq = $contig->get_seq_feat_by_tag($seq,"_aligned_coord:$seqID")
  Function  :
 
              Get a sequence feature based on its primary_tag.
              When you add
 
  Returns   : a Bio::SeqFeature object
  Argument  : a Bio::LocatableSeq and a string (feature primary tag)
 
 

get_seq_by_name

  Title     : get_seq_by_name
  Usage     : $seq = $contig->get_seq_by_name('Seq1')
  Function  : Gets a sequence based on its id.
  Returns   : a Bio::LocatableSeq object
              undef if name is not found
  Argument  : string
 
 

get_qual_by_name

  Title     : get_qual_by_name
  Usage     : $seq = $contig->get_qual_by_name('Seq1')
  Function  :
 
              Gets Bio::Seq::QualI object for a sequence
              through its id ( as given by $qual->id() ).
 
  Returns   : a Bio::Seq::QualI object.
              undef if name is not found
  Argument  : string
 
 

Bio::Align::AlignI compatible methods

Modifier methods

These methods modify the MSE by adding, removing or shuffling complete sequences.

add_seq

  Title     : add_seq
  Usage     : $contig->add_seq($newseq);
  Function  :
 
              Adds a sequence to the contig. *Does*
              *not* align it - just adds it to the
              hashes.
 
  Returns   : nothing
  Argument  : a Bio::LocatableSeq object
 
 

See Bio::LocatableSeq for more information.

remove_seq

  Title     : remove_seq
  Usage     : $contig->remove_seq($seq);
  Function  : Removes a single sequence from a contig
  Returns   : 1 on success, 0 otherwise
  Argument  : a Bio::LocatableSeq object
 
 

purge

  Title   : purge
  Usage   : $contig->purge(0.7);
  Function:
 
            Removes sequences above whatever %id.
 
            This function will grind on large alignments. Beware!
            (perhaps not ideally implemented)
 
  Example :
  Returns : An array of the removed sequences
  Argument:
 
 

sort_alphabetically

  Title     : sort_alphabetically
  Usage     : $contig->sort_alphabetically
  Function  :
 
              Changes the order of the alignemnt to alphabetical on name
              followed by numerical by number.
 
  Returns   :
  Argument  :
 
 

Sequence selection methods

Methods returning one or more sequences objects.

each_seq

  Title     : each_seq
  Usage     : foreach $seq ( $contig->each_seq() )
  Function  : Gets an array of Seq objects from the alignment
  Returns   : an array
  Argument  :
 
 

each_alphabetically

  Title     : each_alphabetically
  Usage     : foreach $seq ( $contig->each_alphabetically() )
  Function  :
 
              Returns an array of sequence object sorted alphabetically
              by name and then by start point.
              Does not change the order of the alignment
 
  Returns   :
  Argument  :
 
 

each_seq_with_id

  Title     : each_seq_with_id
  Usage     : foreach $seq ( $contig->each_seq_with_id() )
  Function  :
 
              Gets an array of Seq objects from the
              alignment, the contents being those sequences
              with the given name (there may be more than one)
 
  Returns   : an array
  Argument  : a seq name
 
 

get_seq_by_pos

  Title     : get_seq_by_pos
  Usage     : $seq = $contig->get_seq_by_pos(3)
  Function  :
 
              Gets a sequence based on its position in the alignment.
              Numbering starts from 1.  Sequence positions larger than
              num_sequences() will thow an error.
 
  Returns   : a Bio::LocatableSeq object
  Argument  : positive integer for the sequence osition
 
 

Create new alignments

The result of these methods are horizontal or vertical subsets of the current MSE.

select

  Title     : select
  Usage     : $contig2 = $contig->select(1, 3) # three first sequences
  Function  :
 
              Creates a new alignment from a continuous subset of
              sequences.  Numbering starts from 1.  Sequence positions
              larger than num_sequences() will thow an error.
 
  Returns   : a Bio::Assembly::Contig object
  Argument  : positive integer for the first sequence
              positive integer for the last sequence to include (optional)
 
 

select_noncont

  Title     : select_noncont
  Usage     : $contig2 = $contig->select_noncont(1, 3) # first and 3rd sequences
  Function  :
 
              Creates a new alignment from a subset of
              sequences.  Numbering starts from 1.  Sequence positions
              larger than num_sequences() will thow an error.
 
  Returns   : a Bio::Assembly::Contig object
  Args      : array of integers for the sequences
 
 

slice

  Title     : slice
  Usage     : $contig2 = $contig->slice(20, 30)
  Function  :
 
              Creates a slice from the alignment inclusive of start and
              end columns.  Sequences with no residues in the slice are
              excluded from the new alignment and a warning is printed.
              Slice beyond the length of the sequence does not do
              padding.
 
  Returns   : a Bio::Assembly::Contig object
  Argument  : positive integer for start column
              positive integer for end column
 
 

Change sequences within the MSE

These methods affect characters in all sequences without changeing the alignment.

map_chars

  Title     : map_chars
  Usage     : $contig->map_chars('\.','-')
  Function  :
 
              Does a s/$arg1/$arg2/ on the sequences. Useful for gap
              characters
 
              Notice that the from (arg1) is interpretted as a regex,
              so be careful about quoting meta characters (eg
              $contig->map_chars('.','-') wont do what you want)
 
  Returns   :
  Argument  : 'from' rexexp
              'to' string
 
 

uppercase

  Title     : uppercase()
  Usage     : $contig->uppercase()
  Function  : Sets all the sequences to uppercase
  Returns   :
  Argument  :
 
 

match_line

  Title    : match_line()
  Usage    : $contig->match_line()
  Function : Generates a match line - much like consensus string
             except that a line indicating the '*' for a match.
  Argument : (optional) Match line characters ('*' by default)
             (optional) Strong match char (':' by default)
             (optional) Weak match char ('.' by default)
 
 

match

  Title     : match()
  Usage     : $contig->match()
  Function  :
 
              Goes through all columns and changes residues that are
              identical to residue in first sequence to match '.'
              character. Sets match_char.
 
              USE WITH CARE: Most MSE formats do not support match
              characters in sequences, so this is mostly for output
              only. NEXUS format (Bio::AlignIO::nexus) can handle
              it.
 
  Returns   : 1
  Argument  : a match character, optional, defaults to '.'
 
 

unmatch

  Title     : unmatch()
  Usage     : $contig->unmatch()
  Function  :
 
              Undoes the effect of method match. Unsets match_char.
 
  Returns   : 1
  Argument  : a match character, optional, defaults to '.'
 
 

MSE attibutes

Methods for setting and reading the MSE attributes.

Note that the methods defining character semantics depend on the user to set them sensibly. They are needed only by certain input/output methods. Unset them by setting to an empty string ('').

id

  Title     : id
  Usage     : $contig->id("Ig")
  Function  : Gets/sets the id field of the alignment
  Returns   : An id string
  Argument  : An id string (optional)
 
 

missing_char

  Title     : missing_char
  Usage     : $contig->missing_char("?")
  Function  : Gets/sets the missing_char attribute of the alignment
              It is generally recommended to set it to 'n' or 'N'
              for nucleotides and to 'X' for protein.
  Returns   : An missing_char string,
  Argument  : An missing_char string (optional)
 
 

match_char

  Title     : match_char
  Usage     : $contig->match_char('.')
  Function  : Gets/sets the match_char attribute of the alignment
  Returns   : An match_char string,
  Argument  : An match_char string (optional)
 
 

gap_char

  Title     : gap_char
  Usage     : $contig->gap_char('-')
  Function  : Gets/sets the gap_char attribute of the alignment
  Returns   : An gap_char string, defaults to '-'
  Argument  : An gap_char string (optional)
 
 

symbol_chars

  Title   : symbol_chars
  Usage   : my @symbolchars = $contig->symbol_chars;
  Function: Returns all the seen symbols (other than gaps)
  Returns : array of characters that are the seen symbols
  Argument: boolean to include the gap/missing/match characters
 
 

Alignment descriptors

These read only methods describe the MSE in various ways.

consensus_string

  Title     : consensus_string
  Usage     : $str = $contig->consensus_string($threshold_percent)
  Function  : Makes a strict consensus
  Returns   :
  Argument  : Optional treshold ranging from 0 to 100.
              The consensus residue has to appear at least threshold %
              of the sequences at a given location, otherwise a '?'
              character will be placed at that location.
              (Default value = 0%)
 
 

consensus_iupac

  Title     : consensus_iupac
  Usage     : $str = $contig->consensus_iupac()
  Function  :
 
              Makes a consensus using IUPAC ambiguity codes from DNA
              and RNA. The output is in upper case except when gaps in
              a column force output to be in lower case.
 
              Note that if your alignment sequences contain a lot of
              IUPAC ambiquity codes you often have to manually set
              alphabet.  Bio::PrimarySeq::_guess_type thinks they
              indicate a protein sequence.
 
  Returns   : consensus string
  Argument  : none
  Throws    : on protein sequences
 
 

is_flush

  Title     : is_flush
  Usage     : if( $contig->is_flush() )
            :
            :
  Function  : Tells you whether the alignment
            : is flush, ie all of the same length
            :
            :
  Returns   : 1 or 0
  Argument  :
 
 

length

  Title     : length()
  Usage     : $len = $contig->length()
  Function  : Returns the maximum length of the alignment.
              To be sure the alignment is a block, use is_flush
  Returns   :
  Argument  :
 
 

maxdname_length

  Title     : maxname_length
  Usage     : $contig->maxname_length()
  Function  :
 
              Gets the maximum length of the displayname in the
              alignment. Used in writing out various MSE formats.
 
  Returns   : integer
  Argument  :
 
 

num_residues

  Title     : num_residues
  Usage     : $no = $contig->num_residues
  Function  : number of residues in total in the alignment
  Returns   : integer
  Argument  :
  Note      : replaces no_residues
 
 

num_sequences

  Title     : num_sequences
  Usage     : $depth = $contig->num_sequences
  Function  : number of sequence in the sequence alignment
  Returns   : integer
  Argument  : None
  Note      : replaces no_sequences
 
 

percentage_identity

  Title   : percentage_identity
  Usage   : $id = $contig->percentage_identity
  Function: The function calculates the percentage identity of the alignment
  Returns : The percentage identity of the alignment (as defined by the
                              implementation)
  Argument: None
 
 

overall_percentage_identity

  Title   : percentage_identity
  Usage   : $id = $contig->percentage_identity
  Function: The function calculates the percentage identity of
            the conserved columns
  Returns : The percentage identity of the conserved columns
  Args    : None
 
 

average_percentage_identity

  Title   : average_percentage_identity
  Usage   : $id = $contig->average_percentage_identity
  Function: The function uses a fast method to calculate the average
            percentage identity of the alignment
  Returns : The average percentage identity of the alignment
  Args    : None
 
 

Alignment positions

Methods to map a sequence position into an alignment column and back. column_from_residue_number() does the former. The latter is really a property of the sequence object and can done using Bio::LocatableSeq::location_from_column:
     # select somehow a sequence from the alignment, e.g.
     my $seq = $contig->get_seq_by_pos(1);
     #$loc is undef or Bio::LocationI object
     my $loc = $seq->location_from_column(5);
 
 

column_from_residue_number

  Title   : column_from_residue_number
  Usage   : $col = $contig->column_from_residue_number( $seqname, $resnumber)
  Function:
 
            This function gives the position in the alignment
            (i.e. column number) of the given residue number in the
            sequence with the given name. For example, for the
            alignment
 
            Seq1/91-97 AC..DEF.GH
            Seq2/24-30 ACGG.RTY..
            Seq3/43-51 AC.DDEFGHI
 
            column_from_residue_number( "Seq1", 94 ) returns 5.
            column_from_residue_number( "Seq2", 25 ) returns 2.
            column_from_residue_number( "Seq3", 50 ) returns 9.
 
            An exception is thrown if the residue number would lie
            outside the length of the aligment
            (e.g. column_from_residue_number( "Seq2", 22 )
 
       Note: If the the parent sequence is represented by more than
       one alignment sequence and the residue number is present in
       them, this method finds only the first one.
 
  Returns : A column number for the position in the alignment of the
            given residue in the given sequence (1 = first column)
  Args    : A sequence id/name (not a name/start-end)
            A residue number in the whole sequence (not just that
            segment of it in the alignment)
 
 

Sequence names

Methods to manipulate the display name. The default name based on the sequence id and subsequence positions can be overridden in various ways.

displayname

  Title     : displayname
  Usage     : $contig->displayname("Ig", "IgA")
  Function  : Gets/sets the display name of a sequence in the alignment
            :
  Returns   : A display name string
  Argument  : name of the sequence
              displayname of the sequence (optional)
 
 

set_displayname_count

  Title     : set_displayname_count
  Usage     : $contig->set_displayname_count
  Function  :
 
              Sets the names to be name_# where # is the number of
              times this name has been used.
 
  Returns   : None
  Argument  : None
 
 

set_displayname_flat

  Title     : set_displayname_flat
  Usage     : $contig->set_displayname_flat()
  Function  : Makes all the sequences be displayed as just their name,
              not name/start-end
  Returns   : 1
  Argument  : None
 
 

set_displayname_normal

  Title     : set_displayname_normal
  Usage     : $contig->set_displayname_normal()
  Function  : Makes all the sequences be displayed as name/start-end
  Returns   : None
  Argument  : None
 
 

Internal Methods

_binary_search

  Title     : _binary_search
  Usage     : _binary_search($list,$query)
  Function  :
 
              Find a number in a sorted list of numbers.  Return values
              may be on or two integers. One positive integer or zero
              (>=0) is the index of the element that stores the queried
              value.  Two positive integers (or zero and another
              number) are the indexes of elements among which the
              queried value should be placed. Negative single values
              mean:
 
              -1: $query is smaller than smallest element in list
              -2: $query is greater than greatest element in list
 
  Returns   : array of integers
  Argument  :
              $list  : array reference
              $query : integer
 
 

_compare

     Title   : _compare
     Usage   : _compare($arg1,$arg2)
     Function: Perform numeric or string comparisons
     Returns : integer (0, 1 or -1)
     Args    : values to be compared
 
 

_nof_gaps

     Title   : _nof_gaps
     Usage   : _nof_gaps($array_ref, $query)
     Function: number of gaps found before position $query
     Returns : integer
     Args    :
               $array_ref : gap registry reference
               $query     : [integer] a position in a sequence
 
 

_padded_unpadded

     Title   : _padded_unpadded
     Usage   : _padded_unpadded($array_ref, $query)
     Function:
 
               Returns a coordinate corresponding to
               position $query after gaps were
               removed from a sequence.
 
     Returns : integer
     Args    :
               $array_ref : reference to this gap registry
               $query     : [integer] coordionate to change
 
 

_unpadded_padded

     Title   : _unpadded_padded
     Usage   : _unpadded_padded($array_ref, $query)
     Function:
 
               Returns the value corresponding to
               ungapped position $query when gaps are
               counted as valid sites in a sequence
 
     Returns :
     Args    : $array_ref = a reference to this sequence's gap registry
               $query = [integer] location to change
 
 

_register_gaps

     Title   : _register_gaps
     Usage   : $self->_register_gaps($seq, $array_ref)
     Function: stores gap locations for a sequence
     Returns : number of gaps found
     Args    :
               $seq       : sequence string
               $array_ref : a reference to an array,
                            where gap locations will
                            be stored
 
 

Deprecated methods

no_residues

  Title     : no_residues
  Usage     : $no = $ali->no_residues
  Function  : number of residues in total in the alignment
  Returns   : integer
  Argument  :
  Note      : deprecated in favor of num_residues()
 
 

no_sequences

  Title     : no_sequences
  Usage     : $depth = $ali->no_sequences
  Function  : number of sequence in the sequence alignment
  Returns   : integer
  Argument  :
  Note      : deprecated in favor of num_sequences()