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Bio/Align/AlignI.pm view on Meta::CPAN
#
# BioPerl module for Bio::Align::AlignI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Align::AlignI - An interface for describing sequence alignments.
=head1 SYNOPSIS
# get a Bio::Align::AlignI somehow - typically using Bio::AlignIO system
# some descriptors
print $aln->length, "\n";
print $aln->num_residues, "\n";
print $aln->is_flush, "\n";
print $aln->num_sequences, "\n";
print $aln->percentage_identity, "\n";
print $aln->consensus_string(50), "\n";
# find the position in the alignment for a sequence location
$pos = $aln->column_from_residue_number('1433_LYCES', 14); # = 6;
# extract sequences and check values for the alignment column $pos
foreach $seq ($aln->each_seq) {
$res = $seq->subseq($pos, $pos);
$count{$res}++;
}
foreach $res (keys %count) {
printf "Res: %s Count: %2d\n", $res, $count{$res};
}
=head1 DESCRIPTION
This interface describes the basis for alignment objects.
=head1 FEEDBACK
=head2 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 list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 CONTRIBUTORS
Ewan Birney, birney@ebi.ac.uk
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub missing_char {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 match_char
Title : match_char
Usage : $myalign->match_char('.')
Function : Gets/sets the match_char attribute of the alignment
Returns : An match_char string,
Argument : An match_char string (optional)
=cut
sub match_char {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 gap_char
Title : gap_char
Usage : $myalign->gap_char('-')
Function : Gets/sets the gap_char attribute of the alignment
Returns : An gap_char string, defaults to '-'
Argument : An gap_char string (optional)
=cut
sub gap_char {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 symbol_chars
Title : symbol_chars
Usage : my @symbolchars = $aln->symbol_chars;
Function: Returns all the seen symbols (other than gaps)
Returns : array of characters that are the seen symbols
Argument: boolean to include the gap/missing/match characters
=cut
sub symbol_chars{
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 Alignment descriptors
These read only methods describe the MSE in various ways.
=head2 consensus_string
Title : consensus_string
Usage : $str = $ali->consensus_string($threshold_percent)
Function : Makes a strict consensus
Returns : consensus string
Argument : Optional threshold 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%)
=cut
sub consensus_string {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 consensus_iupac
Title : consensus_iupac
Usage : $str = $ali->consensus_iupac()
Function :
Makes a consensus using IUPAC ambiguity codes from DNA
and RNA. The output is in upper case except when gaps in
a column force output to be in lower case.
Note that if your alignment sequences contain a lot of
IUPAC ambiquity codes you often have to manually set
alphabet. Bio::PrimarySeq::_guess_type thinks they
indicate a protein sequence.
Returns : consensus string
Argument : none
Throws : on protein sequences
=cut
sub consensus_iupac {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 is_flush
Title : is_flush
Usage : if( $ali->is_flush() )
:
:
Function : Tells you whether the alignment
: is flush, ie all of the same length
:
:
Returns : 1 or 0
Argument :
=cut
sub is_flush {
my ($self) = @_;
$self->throw_not_implemented();
Bio/Align/AlignI.pm view on Meta::CPAN
Argument :
=cut
sub length {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 maxname_length
Title : maxname_length
Usage : $ali->maxname_length()
Function :
Gets the maximum length of the displayname in the
alignment. Used in writing out various MSE formats.
Returns : integer
Argument :
=cut
sub maxname_length {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 num_residues
Title : num_residues
Usage : $no = $ali->num_residues
Function : number of residues in total in the alignment
Returns : integer
Argument :
Note : replaces no_residues
=cut
sub num_residues {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 num_sequences
Title : num_sequences
Usage : $depth = $ali->num_sequences
Function : number of sequence in the sequence alignment
Returns : integer
Argument : None
Note : replaces no_sequences
=cut
sub num_sequences {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 percentage_identity
Title : percentage_identity
Usage : $id = $align->percentage_identity
Function: The function calculates the percentage identity of the alignment
Returns : The percentage identity of the alignment (as defined by the
implementation)
Argument: None
=cut
sub percentage_identity{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 overall_percentage_identity
Title : overall_percentage_identity
Usage : $id = $align->overall_percentage_identity
Function: The function calculates the percentage identity of
the conserved columns
Returns : The percentage identity of the conserved columns
Args : None
=cut
sub overall_percentage_identity{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 average_percentage_identity
Title : average_percentage_identity
Usage : $id = $align->average_percentage_identity
Function: The function uses a fast method to calculate the average
percentage identity of the alignment
Returns : The average percentage identity of the alignment
Args : None
=cut
sub average_percentage_identity{
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 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
L<Bio::LocatableSeq::location_from_column>:
# select somehow a sequence from the alignment, e.g.
my $seq = $aln->get_seq_by_pos(1);
#$loc is undef or Bio::LocationI object
my $loc = $seq->location_from_column(5);
=head2 column_from_residue_number
Title : column_from_residue_number
Usage : $col = $ali->column_from_residue_number( $seqname, $resnumber)
Function:
This function gives the position in the alignment
(i.e. column number) of the given residue number in the
sequence with the given name. For example, for the
alignment
Seq1/91-97 AC..DEF.GH
Seq2/24-30 ACGG.RTY..
Seq3/43-51 AC.DDEFGHI
column_from_residue_number( "Seq1", 94 ) returns 6.
column_from_residue_number( "Seq2", 25 ) returns 2.
column_from_residue_number( "Seq3", 50 ) returns 9.
An exception is thrown if the residue number would lie
outside the length of the alignment
(e.g. column_from_residue_number( "Seq2", 22 )
Note: If the parent sequence is represented by more than one
alignment sequence and the residue number is present in
them, this method finds only the first one.
Returns : A column number for the position in the alignment of the
given residue in the given sequence (1 = first column)
Args : A sequence id/name (not a name/start-end)
A residue number in the whole sequence (not just that
segment of it in the alignment)
=cut
sub column_from_residue_number {
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 Sequence names
Methods to manipulate the display name. The default name based on the
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