Bio::Assembly
Contig
Summary
Bio::Assembly::Contig - Perl module to hold and manipulate
sequence assembly contigs.
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Included modules
Inherit
Synopsis
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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.
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 $seqID"), the
position returned will be the first location before all gaps
neighboring the input location.
Bio::Assembly::Contig stores much information about a contig in a
Bio::Assembly::SeqFeature::Collection object. Relevant information on the
alignment is accessed by selecting features based on their primary
tags (e.g. all features which have a primary tag of the form
'_aligned_coord:$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.
Methods
Methods description
Title : new
Usage : my $contig = new Bio::Assembly::Contig();
Function : Creates a new contig object
Returns : Bio::Assembly::Contig
Args : -source => string representing the source
program where this contig came
from
-id => contig unique ID |
Title : source
Usage : $contig->source($program);
Function : Get/Set program used to build this contig
Returns : string
Argument : [optional] string |
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 |
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 |
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 |
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 |
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. |
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 |
Title : get_features_collection
Usage : $contig->get_features_collection()
Function : Get the collection of all contig features
Returns : Bio::SeqFeature::Collection
Argument : none |
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 |
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 |
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 |
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 |
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 |
Title : get_consensus_length
Usage : $contig->get_consensus_length()
Function : Get consensus sequence length
Returns : integer
Argument : none |
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 |
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 |
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. |
Title : get_seq_ids
Usage : $contig->get_seq_ids(-start=>$start,
-end=>$end,
-type=>"gapped A0QR67B08.b");
Function : Get list of sequence IDs overlapping inteval [$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 |
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) |
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 |
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 |
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. |
Title : remove_seq
Usage : $contig->remove_seq($seq);
Function : Removes a single sequence from an alignment
Returns : 1 on success, 0 otherwise
Argument : a Bio::LocatableSeq object |
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: |
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 : |
Title : each_seq
Usage : foreach $seq ( $contig->each_seq() )
Function : Gets an array of Seq objects from the alignment
Returns : an array
Argument : |
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 : |
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 |
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
no_sequences() will thow an error.
Returns : a Bio::LocatableSeq object
Argument : positive integer for the sequence osition |
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 no_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) |
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 no_sequences() will thow an error.
Returns : a Bio::Assembly::Contig object
Args : array of integers for the sequences |
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 |
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 |
Title : uppercase()
Usage : $contig->uppercase()
Function : Sets all the sequences to uppercase
Returns :
Argument : |
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) |
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 '.' |
Title : unmatch()
Usage : $contig->unmatch()
Function :
Undoes the effect of method match. Unsets match_char.
Returns : 1
Argument : a match character, optional, defaults to '.' |
Title : id
Usage : $contig->id("Ig")
Function : Gets/sets the id field of the alignment
Returns : An id string
Argument : An id string (optional) |
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) |
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) |
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) |
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 |
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%) |
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 |
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 : |
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 : |
Title : no_residues
Usage : $no = $contig->no_residues
Function : number of residues in total in the alignment
Returns : integer
Argument : |
Title : no_sequences
Usage : $depth = $contig->no_sequences
Function : number of sequence in the sequence alignment
Returns : integer
Argument : None |
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 |
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 |
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 |
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) |
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) |
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 |
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 |
Title : set_displayname_normal
Usage : $contig->set_displayname_normal()
Function : Makes all the sequences be displayed as name/start-end
Returns : None
Argument : None |
Title : _binary_search
Usage : _binary_search($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
$query : integer |
Title : _compare
Usage : _compare($arg1,$arg2)
Function: Perform numeric or string comparisons
Returns : integer (0, 1 or -1)
Args : values to be compared |
Title : _nof_gaps
Usage : _nof_gaps($array_ref, $query)
Function: number of gaps found before position $query
Returns : integer
Args :
$array_ref : gap registry reference
$query : [integer] a position in a sequence |
Title : _padded_unpadded
Usage : _padded_unpadded($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
$query : [integer] coordionate to change |
Title : _unpadded_padded
Usage : _unpadded_padded($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 |
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
$array_ref : a reference to an array,
where gap locations will
be stored |
Methods code
sub new
{
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($src, $id) = $self->_rearrange([qw(SOURCE ID)], @args);
$src && $self->source($src);
($id && $self->id($id)) || ($self->{'_id'} = 'NoName');
($id && $self->id($id)) || ($self->{'_source'} = 'Unknown');
$self->{'_elem'} = {};
$self->{'_order'} = {};
$self->{'_symbols'} = {};
$self->{'_consensus_sequence'} = undef;
$self->{'_consensus_quality'} = undef;
$self->{'_nof_residues'} = 0;
$self->{'_nof_seqs'} = 0;
$self->{'_sfc'} = Bio::SeqFeature::Collection->new();
$self->{'_assembly'} = undef;
$self->{'_strand'} = 0;
$self->{'_neighbor_start'} = undef;
$self->{'_neighbor_end'} = undef;
return $self;
} | sub source
{ my $self = shift;
my $source = shift;
$self->{'_source'} = $source if (defined $source);
return $self->{'_source'};} | sub assembly
{ my $self = shift;
my $assembly = shift;
$self->throw("Using non Bio::Assembly::Scaffold object when assign contig to assembly")
if (defined $assembly && ! $assembly->isa("Bio::Assembly::Scaffold"));
$self->{'_assembly'} = $assembly if (defined $assembly);
return $self->{'_assembly'};} | sub strand
{ my $self = shift;
my $ori = shift;
$self->throw("Contig strand must be either 1, -1 or 0")
unless (defined $ori && ($ori == 1 || $ori == 0 || $ori == -1));
$self->{'_strand'} = $ori;
return $self->{'_strand'};} | sub upstream_neighbor
{ my $self = shift;
my $ref = shift;
$self->throw("Trying to assign a non Bio::Assembly::Contig object to upstream contig")
if (defined $ref && ! $ref->isa("Bio::Assembly::Contig"));
$self->{'_neighbor_start'} = $ref if (defined $ref);
return $self->{'_neighbor_start'};} | sub downstream_neighbor
{ my $self = shift;
my $ref = shift;
$self->throw("Trying to assign a non Bio::Assembly::Contig object to downstream contig")
if (defined $ref && ! $ref->isa("Bio::Assembly::Contig"));
$self->{'_neighbor_end'} = $ref if (defined $ref);
return $self->{'_neighbor_end'};} | sub add_features
{ my ($self, $args, $flag) = @_;
$flag = 0 unless (defined $flag);
if ($flag && defined $self->{'_consensus_sequence'}) {
foreach my $feat (@$args) {
next if (defined $feat->seq);
$feat->attach_seq($self->{'_consensus_sequence'});
}
} elsif (!$flag) {
foreach my $feat (@$args) {
if (my $seq = $feat->entire_seq()) {
my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
$self->warn("Adding contig feature attached to unknown sequence $seqID!")
unless (exists $self->{'_elem'}{$seqID});
my $tag = $feat->primary_tag;
$self->{'_elem'}{$seqID}{'_feat'}{$tag} = $feat;
}
}
}
my $nof_added = $self->{'_sfc'}->add_features($args);
return $nof_added;} | sub remove_features
{ my ($self, @args) = @_;
foreach my $feat (@args) {
if (my $seq = $feat->entire_seq()) {
my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
my $tag = $feat->primary_tag;
$tag =~ s/:$seqID$/$1/g;
delete( $self->{'_elem'}{$seqID}{'_feat'}{$tag} )
if (exists $self->{'_elem'}{$seqID}{'_feat'}{$tag} &&
$self->{'_elem'}{$seqID}{'_feat'}{$tag} eq $feat);
}
}
return $self->{'_sfc'}->remove_features(\@args);} | sub get_features_collection
{ my $self = shift;
return $self->{'_sfc'};} | sub change_coord
{ my $self = shift;
my $type_in = shift;
my $type_out = shift;
my $query = shift;
my ($read_in,$read_out) = (undef,undef);
my $in_ID = ( split(' ',$type_in) )[1];
my $out_ID = ( split(' ',$type_out) )[1];
if ($in_ID ne 'consensus') {
$read_in = $self->get_seq_coord( $self->get_seq_by_name($in_ID) );
$self->throw("Can't change coordinates without sequence location for $in_ID")
unless (defined $read_in);
}
if ($out_ID ne 'consensus') {
$read_out = $self->get_seq_coord( $self->get_seq_by_name($out_ID) );
$self->throw("Can't change coordinates without sequence location for $out_ID")
unless (defined $read_out);
}
SWITCH1: {
(($type_in eq 'gapped consensus') && ($type_out eq 'ungapped consensus')) && do {
$self->throw("Can't use ungapped consensus coordinates without a consensus sequence")
unless (defined $self->{'_consensus_sequence'});
$query = &_padded_unpadded($self->{'_consensus_gaps'}, $query);
last SWITCH1;
};
(($type_in eq 'ungapped consensus') && ($type_out eq 'gapped consensus')) && do {
$self->throw("Can't use ungapped consensus coordinates without a consensus sequence")
unless (defined $self->{'_consensus_sequence'});
$query = &_unpadded_padded($self->{'_consensus_gaps'},$query);
last SWITCH1;
};
(($type_in eq 'gapped consensus') &&
($type_out =~ /^aligned /) && defined($read_out)) && do {
$query = $query - $read_out->start() + 1;
last SWITCH1;
};
(($type_in =~ /^aligned /) && defined($read_in) &&
($type_out eq 'gapped consensus')) && do {
$query = $query + $read_in->start() - 1;
last SWITCH1;
};
(($type_in eq 'ungapped consensus') &&
($type_out =~ /^aligned /) && defined($read_out)) && do {
$query = $self->change_coord('ungapped consensus','gapped consensus',$query);
$query = $self->change_coord('gapped consensus',"aligned $out_ID",$query);
last SWITCH1;
};
(($type_in =~ /^aligned /) && defined($read_in) &&
($type_out eq 'ungapped consensus')) && do {
$query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
$query = $self->change_coord('gapped consensus','ungapped consensus',$query);
last SWITCH1;
};
(defined($read_in) && ($type_in =~ /^aligned /) &&
defined($read_out) && ($type_out =~ /^aligned /)) && do {
$query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
$query = $self->change_coord('gapped consensus',"aligned $out_ID",$query);
last SWITCH1;
};
(defined($read_in) && ($type_in =~ /^aligned /) &&
defined($read_out) && ($type_out =~ /^unaligned /)) && do {
if ($read_in ne $read_out) {
$query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
$query = $self->change_coord('gapped consensus',"aligned $out_ID",$query);
}
my $list_out = $self->{'_elem'}{$out_ID}{'_gaps'};
$query = &_padded_unpadded($list_out,$query);
if ($read_out->strand == -1) {
my ($length) = $read_out->length();
$length = $length - &_nof_gaps($list_out,$length);
$query = $length - $query + 1;
}
last SWITCH1;
};
(defined($read_in) && ($type_in =~ /^unaligned /) &&
defined($read_out) && ($type_out =~ /^aligned /)) && do {
my $list_in = $self->{'_elem'}{$in_ID}{'_gaps'};
if ($read_in->strand == -1) {
my ($length) = $read_in->length();
$length = $length - &_nof_gaps($list_in,$length);
$query = $length - $query + 1;
}
$query = &_unpadded_padded($list_in,$query);
if ($read_in ne $read_out) {
$query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
$query = $self->change_coord('gapped consensus',"aligned $out_ID",$query);
}
last SWITCH1;
};
(defined($read_in) && ($type_in =~ /^unaligned /) &&
defined($read_out) && ($type_out =~ /^unaligned /)) && do {
$query = $self->change_coord("unaligned $in_ID","aligned $out_ID",$query);
$query = $self->change_coord("aligned $out_ID","unaligned $out_ID",$query);
last SWITCH1;
};
(($type_in eq 'gapped consensus') &&
($type_out =~ /^unaligned /) && defined($read_out)) && do {
$query = $self->change_coord('gapped consensus',"aligned $out_ID",$query);
$query = $self->change_coord("aligned $out_ID","unaligned $out_ID",$query);
last SWITCH1;
};
(($type_in =~ /^unaligned /) && defined($read_in) &&
($type_out eq 'gapped consensus')) && do {
$query = $self->change_coord("unaligned $in_ID","aligned $in_ID",$query);
$query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
last SWITCH1;
};
(($type_in eq 'ungapped consensus') &&
($type_out =~ /^unaligned /) && defined($read_out)) && do {
$query = $self->change_coord('ungapped consensus','gapped consensus',$query);
$query = $self->change_coord('gapped consensus',"unaligned $out_ID",$query);
last SWITCH1;
};
(($type_in =~ /^unaligned /) && defined($read_in) &&
($type_out eq 'ungapped consensus')) && do {
$query = $self->change_coord("unaligned $in_ID",'gapped consensus',$query);
$query = $self->change_coord('gapped consensus','ungapped consensus',$query);
last SWITCH1;
};
$self->throw("Unknow coordinate system. Args: $type_in, $type_out.");
$query = undef;
}
return $query;} | sub get_seq_coord
{ my ($self,$seq) = @_;
if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) {
$self->throw("$seq is not a Bio::LocatableSeq");
}
my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
unless (exists( $self->{'_elem'}{$seqID} )) {
$self->warn("No such sequence ($seqID) in contig ".$self->id);
return undef;
}
unless (exists( $self->{'_elem'}{$seqID}{'_feat'}{"_aligned_coord:$seqID"} )) {
$self->warn("Location not set for sequence ($seqID) in contig ".$self->id);
return undef;
}
return $self->{'_elem'}{$seqID}{'_feat'}{"_aligned_coord:$seqID"};} | sub set_seq_coord
{ my ($self,$feat,$seq) = @_;
if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) {
$self->throw("Unable to process non locatable sequences [".ref($seq)."]");
}
$self->throw("Coordinates must be a Bio::SeqFeature::Generic object!")
unless ( $feat->isa("Bio::SeqFeature::Generic") );
$self->throw("Sequence coordinates must have an end!")
unless (defined $feat->end);
$self->throw("Sequence coordinates must have a start!")
unless (defined $feat->start);
my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
if (exists( $self->{'_elem'}{$seqID} ) &&
exists( $self->{'_elem'}{$seqID}{'_seq'} ) &&
defined( $self->{'_elem'}{$seqID}{'_seq'} ) &&
($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) {
$self->warn("Replacing sequence $seqID\n");
$self->remove_seq($self->{'_elem'}{$seqID}{'_seq'});
}
$self->add_seq($seq);
$self->remove_features($feat);
$feat->add_tag_value('contig',$self->id)
unless ( $feat->has_tag('contig') );
$feat->primary_tag("_aligned_coord:$seqID");
$feat->attach_seq($seq);
$self->{'_elem'}{$seqID}{'_feat'}{"_aligned_coord:$seqID"} = $feat;
$self->add_features([ $feat ]);} | sub set_consensus_sequence
{ my $self = shift;
my $seq = shift;
$self->throw("Consensus sequence must be a Bio::LocatableSeq!")
unless ($seq->isa("Bio::LocatableSeq"));
my $con_len = $seq->length;
$seq->start(1); $seq->end($con_len);
$self->{'_consensus_gaps'} = [];
$self->_register_gaps($seq->seq,
$self->{'_consensus_gaps'});
$self->{'_consensus_sequence'} = $seq;
return $con_len;} | sub set_consensus_quality
{ my $self = shift;
my $qual = shift;
$self->throw("Consensus quality must be a Bio::Seq::QualI object!")
unless ( $qual->isa("Bio::Seq::QualI") );
$self->throw("Consensus quality can't be added before you set the consensus sequence!")
unless (defined $self->{'_consensus_sequence'});
$self->{'_consensus_quality'} = $qual;} | sub get_consensus_length
{ my $self = shift;
return $self->{'_consensus_sequence'}->length();} | sub get_consensus_sequence
{ my ($self, @args) = @_;
return $self->{'_consensus_sequence'};} | sub get_consensus_quality
{ my ($self, @args) = @_;
return $self->{'_consensus_quality'};} | sub set_seq_qual
{ my ($self,$seq,$qual) = @_;
if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) {
$self->throw("Unable to process non locatable sequences [", ref($seq), "]");
}
my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
$self->throw("Consensus quality must be a Bio::Seq::QualI object!")
unless ( $qual->isa("Bio::Seq::QualI") );
$self->throw("Use add_seq first: aligned sequence qualities can't be added before you load the sequence!")
unless (exists $self->{'_elem'}{$seqID}{'_seq'});
$self->throw("Use set_seq_coord first: aligned sequence qualities can't be added before you add coordinates for the sequence!") unless (defined( $self->get_seq_coord($seq) ));
my $sequence = $self->{'_elem'}{$seqID}{'_seq'}->seq();
my $tmp = $qual->qual();
@{$tmp} = reverse(@{$tmp}) if ($self->get_seq_coord($seq)->strand() == -1);
my @quality = ();
my $previous = 0;
my $next = 0;
my $i = 0; my $j = 0;
while ($i<=$#{$tmp}) {
if (substr($sequence,$j,1) eq '-') {
$previous = $tmp->[$i-1] unless ($i == 0);
if ($i < $#{$tmp}) {
$next = $tmp->[$i+1];
} else {
$next = 0;
}
push(@quality,int( ($previous+$next)/2 ));
} else {
push(@quality,$tmp->[$i]);
$i++;
}
$j++;
}
$self->{'_elem'}{$seqID}{'_qual'} = Bio::Seq::PrimaryQual->new(-qual=>join(" ",@quality),
-id=>$seqID);} | sub get_seq_ids
{ my ($self, @args) = @_;
my ($type,$start,$end) =
$self->_rearrange([qw(TYPE START END)], @args);
if (defined($start) && defined($end)) {
if (defined($type) && ($type ne 'gapped consensus')) {
$start = $self->change_coord($type,'gapped consensus',$start);
$end = $self->change_coord($type,'gapped consensus',$end);
}
my @list = grep { $_->isa("Bio::SeqFeature::Generic") &&
($_->primary_tag =~ /^_aligned_coord:/) }
$self->{'_sfc'}->features_in_range(-start=>$start,
-end=>$end,
-contain=>0,
-strandmatch=>'ignore');
@list = map { $_->entire_seq->id } @list;
return @list;
}
return map { $self->{'_order'}{$_} } sort { $a cmp $b } keys %{ $self->{'_order'} };} | sub get_seq_feat_by_tag
{ my ($self,$seq,$tag) = @_;
if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) {
$self->throw("Unable to process non locatable sequences [", ref($seq), "]");
}
my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
return $self->{'_elem'}{$seqID}{'_feat'}{$tag};} | sub get_seq_by_name
{ my $self = shift;
my ($seqID) = @_;
unless (exists $self->{'_elem'}{$seqID}{'_seq'}) {
$self->throw("Could not find sequence $seqID in contig ".$self->id);
return undef;
}
return $self->{'_elem'}{$seqID}{'_seq'};} | sub get_qual_by_name
{ my $self = shift;
my ($seqID) = @_;
unless (exists $self->{'_elem'}{$seqID}{'_qual'}) {
$self->warn("Could not find quality for $seqID in contig!");
return undef;
}
return $self->{'_elem'}{$seqID}{'_qual'};} | sub add_seq
{ my $self = shift;
my $seq = shift;
if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) {
$self->throw("Unable to process non locatable sequences [", ref($seq), "]");
}
my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
$self->{'_elem'}{$seqID} = {} unless (exists $self->{'elem'}{$seqID});
if (exists( $self->{'_elem'}{$seqID}{'_seq'} ) &&
($seq eq $self->{'_elem'}{$seqID}{'_seq'}) ) {
$self->warn("Adding sequence $seqID, which has already been added");
}
$seq->start(1); $seq->end($seq->length());
$self->warn("Adding non-nucleotidic sequence ".$seqID)
if (lc($seq->alphabet) ne 'dna' && lc($seq->alphabet) ne 'rna');
if (defined $seq->seq) {
map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq);
} else {
$self->{'_symbols'} = {};
}
my $seq_no = ++$self->{'_nof_seqs'};
if (ref( $self->{'_elem'}{$seqID}{'_seq'} )) {
$self->warn("Replacing one sequence [$seqID]\n");
} else {
$self->{'_order'}->{$seq_no} = $seqID;
}
$self->{'_elem'}{$seqID}{'_seq'} = $seq;
$self->{'_elem'}{$seqID}{'_feat'} = {};
$self->{'_elem'}{$seqID}{'_gaps'} = [];
my $dbref = $self->{'_elem'}{$seqID}{'_gaps'};
my $nofgaps = $self->_register_gaps($seq->seq,$dbref);
$self->{'_nof_residues'} += $seq->length - $nofgaps;
return 1;} | sub remove_seq
{ my ($self,$seq) = @_;
if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) {
$self->throw("Unable to process non locatable sequences [", ref($seq), "]");
}
my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
unless (exists $self->{'_elem'}{$seqID} ) {
$self->warn("No sequence named $seqID [$seq]");
return 0;
}
$self->{'_nof_residues'} -= $seq->length() +
&_nof_gaps( $self->{'_elem'}{$seqID}{'_gaps'}, $seq->length );
my @feats = ();
foreach my $tag (keys %{ $self->{'_elem'}{$seqID}{'_feat'} }) {
push(@feats, $self->{'_elem'}{$seqID}{'_feat'}{$tag});
}
$self->{'_sfc'}->remove_features(\@feats);
delete $self->{'_elem'}{$seqID};
return 1;} | sub purge
{ my ($self) = @_;
$self->throw_not_implemented();} | sub sort_alphabetically
{ my ($self) = @_;
$self->throw_not_implemented();} | sub each_seq
{ my ($self) = @_;
my (@arr,$seqID);
foreach $seqID ( map { $self->{'_order'}{$_} } sort { $a <=> $b } keys %{$self->{'_order'}} ) {
push(@arr,$self->{'_elem'}{$seqID}{'_seq'});
}
return @arr;} | sub each_alphabetically
{ my($self) = @_;
$self->throw_not_implemented();} | sub each_seq_with_id
{ my ($self) = @_;
$self->throw_not_implemented();} | sub get_seq_by_pos
{ my $self = shift;
my ($pos) = @_;
$self->throw("Sequence position has to be a positive integer, not [$pos]")
unless $pos =~ /^\d+$/ and $pos > 0;
$self->throw("No sequence at position [$pos]")
unless $pos <= $self->no_sequences ;
my $seqID = $self->{'_order'}->{--$pos};
return $self->{'_elem'}{$seqID}{'_seq'};} | sub select
{ my ($self) = @_;
$self->throw_not_implemented();} | sub select_noncont
{ my ($self) = @_;
$self->throw_not_implemented();} | sub slice
{ my ($self) = @_;
$self->throw_not_implemented();} | sub map_chars
{ my ($self) = @_;
$self->throw_not_implemented();} | sub uppercase
{ my ($self) = @_;
$self->throw_not_implemented();} | sub match_line
{ my ($self) = @_;
$self->throw_not_implemented();} | sub match
{ my ($self) = @_;
$self->throw_not_implemented();} | sub unmatch
{ my ($self) = @_;
$self->throw_not_implemented();} | sub id
{ my ($self, $contig_name) = @_;
if (defined( $contig_name )) {
$self->{'_id'} = $contig_name;
}
return $self->{'_id'};} | sub missing_char
{ my ($self) = @_;
$self->throw_not_implemented();} | sub match_char
{ my ($self) = @_;
$self->throw_not_implemented();} | sub gap_char
{ my ($self) = @_;
$self->throw_not_implemented();} | sub symbol_chars
{ my ($self) = @_;
$self->throw_not_implemented();} | sub consensus_string
{ my ($self) = @_;
$self->throw_not_implemented();} | sub consensus_iupac
{ my ($self) = @_;
$self->throw_not_implemented();} | sub is_flush
{ my ($self) = @_;
$self->throw_not_implemented();} | sub length
{ my ($self) = @_;
$self->throw_not_implemented();} | sub maxname_length
{ my ($self) = @_;
$self->throw_not_implemented();} | sub no_residues
{ my ($self) = @_;
return $self->{'_nof_residues'};} | sub no_sequences
{ my ($self) = @_;
return scalar( keys %{ $self->{'_elem'} } );} | sub percentage_identity
{ my ($self) = @_;
$self->throw_not_implemeneted();} | sub overall_percentage_identity
{ my ($self) = @_;
$self->throw_not_implemented();} | sub average_percentage_identity
{ my ($self) = @_;
$self->throw_not_implemented();} | sub column_from_residue_number
{ my ($self) = @_;
$self->throw_not_implemented();} | sub set_displayname_count
{ my ($self) = @_;
$self->throw_not_implemented();} | sub set_displayname_flat
{ } | sub set_displayname_normal
{ } | sub _binary_search
{ my $list = shift;
my $query = shift;
if (!$#{$list} && ($query == $list->[0])) { return (0) }
my $start = 0;
my $end = $#{$list};
(&_compare($query,$list->[$start]) == 0) && do { return ($start) };
(&_compare($query,$list->[$end]) == 0) && do { return ($end) };
(&_compare($query,$list->[$start]) < 0) && do { return (-1) };
(&_compare($query,$list->[$end]) > 0) && do { return (-2) };
my $middle = 0;
while ($end - $start > 1) {
$middle = int(($end+$middle)/2);
(&_compare($query,$list->[$middle]) == 0) && return ($middle);
(&_compare($query,$list->[$middle]) < 0) && do { $end = $middle ; $middle = 0; next };
$start = $middle;
}
return ($start,$end);} | sub _compare
{ my $arg1 = shift;
my $arg2 = shift;
if (($arg1 =~ /^\d+$/) && ($arg2 =~ /^\d+$/)) { return $arg1 <=> $arg2 }
else { return $arg1 cmp $arg2 }} | sub _nof_gaps
{ my $list = shift;
my $query = shift;
return 0 unless (defined($list) && scalar(@{$list}));
my @index = &_binary_search($list,$query);
if ($index[0] == -2) { $query = scalar(@{$list}) }
elsif ($index[0] == -1) { $query = 0 }
elsif ($index[0] >= 0) {
if ($#index > 0) { $query = $index[0] + 1 }
elsif ($#index == 0) { $query = $index[0] }
}
return $query;} | sub _padded_unpadded
{ my $list = shift;
my $query = shift;
my $align = &_nof_gaps($list,$query);
$query-- if (defined($list->[$align]) && ($list->[$align] == $query));
$query = $query - $align;
return $query;} | sub _unpadded_padded
{ my $list = shift;
my $query = shift;
my $align = &_nof_gaps($list,$query);
$query = $query + $align;
my $new_align = &_nof_gaps($list,$query);
while ($new_align - $align > 0) {
$query = $query + $new_align - $align;
$align = $new_align;
$new_align = &_nof_gaps($list,$query);
}
while (defined($list->[$align]) && ($list->[$align] == $query)) {
$query++; $align++;
}
return $query;} | sub _register_gaps
{ my $self = shift;
my $sequence = shift;
my $dbref = shift;
$self->throw("Not an aligned sequence string to register gaps")
if (ref($sequence));
$self->throw("Not an array reference for gap registry")
unless (ref($dbref) eq 'ARRAY');
@{$dbref} = ();
if (defined $sequence) {
my $i = -1;
while(1) {
$i = index($sequence,"-",$i+1);
last if ($i == -1);
push(@{$dbref},$i+1);
}
} else {
return 0;
}
return scalar(@{$dbref});} | General documentation
# Module loading
use Bio::Assembly::IO;
# Assembly loading methods
$aio = new Bio::Assembly::IO(-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";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://bio.perl.org/MailList.html - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
| AUTHOR - Robson Francisco de Souza | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
| Assembly related methods | Top |
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.
| Contig feature collection methods | Top |
| Coordinate system's related methods | Top |
| Bio::Assembly::Contig consensus methods | Top |
| Bio::Assembly::Contig aligned sequences methods | Top |
| Bio::Align::AlignI compatible methods | Top |
These methods modify the MSE by adding, removing or shuffling complete
sequences.
| Sequence selection methods | Top |
Methods returning one or more sequences objects.
The result of these methods are horizontal or vertical subsets of the
current MSE.
| Change sequences within the MSE | Top |
These methods affect characters in all sequences without changeing the
alignment.
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 ('').
These read only methods describe the MSE in various ways.
Title : maxdisplayname_length
Usage : $contig->maxdisplayname_length()
Function :
Gets the maximum length of the displayname in the
alignment. Used in writing out various MSE formats.
Returns : integer
Argument :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);Methods to manipulate the display name. The default name based on the
sequence id and subsequence positions can be overridden in various
ways.