Provided by: gbrowse_2.56+dfsg-11_all 
NAME
Bio::Graphics::Browser2::PadAlignment - Insert pads into a multiple alignment
VERSION (CVS-info)
$RCSfile: PadAlignment.pm,v $
$Revision$
$Author: lstein $
$Date: 2008-09-09 20:53:36 $
SYNOPSIS
use Bio::Graphics::Browser2::PadAlignment;
my @dnas = (
dna1 =>'FFFFgatcGATCgatcGATCgatcGATCgatcGBATCgatcGATCatcGATCgatcGATCgatcGATCgatcGATgatcGATCgatcNNNNGATC',
dna2 =>'FFgatcGATCGATCgatcNNGATCgatcGATCgatcGATCgatcGATCgatcGATCtcGATBCgatcGATCatcGATCgatcNNNNGATCFFFF',
dna3 =>'FFFFgatcGATCgatcGATCgatcGATCgatcBBBGATCgatcGATCatcGATCBgatcGATCgatcGATCgatcGATgatcGATCgatcNNNNGATCFF',
dna4 =>'ZZFFFFgatcGATCgatcGATCgatcGATCgatc',
dna5 =>'ATBGGATtcttttttt',
);
# target st en tst ten
my @alignments = ([ 'dna2', 4, 11, 2, 9 ],
[ 'dna2', 16, 23, 10, 17 ],
[ 'dna2', 24, 32, 20, 28 ],
[ 'dna2', 34, 44, 29, 39 ],
[ 'dna2', 45, 59, 41, 55 ],
[ 'dna2', 62, 66, 56, 60 ],
[ 'dna2', 67, 74, 62, 69 ],
[ 'dna2', 76, 86, 71, 81 ],
[ 'dna2', 91, 94, 86, 89 ],
[ 'dna3', 4, 31, 4, 31 ],
[ 'dna3', 33, 33, 34, 34 ],
[ 'dna3', 34, 51, 36, 53 ],
[ 'dna3', 52, 86, 55, 89 ],
[ 'dna3', 91, 94, 94, 97 ],
[ 'dna4', 0, 31, 2, 33 ],
[ 'dna5', 17, 18, 0, 1 ],
[ 'dna5', 41, 43, 4, 6 ],
[ 'dna5', 85, 86, 7, 8 ],
);
my $align = Bio::Graphics::Browser2::PadAlignment->new(\@dnas,\@alignments);
my @padded = $align->padded_sequences;
print join "\n",@padded,"\n";
# ..FFFFgatcGATCgatcGATCgatc--GATCgatcG-B-ATCgatcGATC-atcGATC-gatcGATCgatcGAT-CgatcGATgatcGATCgatcNNNNGATC....
# ....FFgatcGATC----GATCgatcNNGATCgatcG---ATCgatcGATCgatcGATC-gatcGATC--tcGATBCgatcGATCatcGATCgatcNNNNGATCFFFF
# ..FFFFgatcGATCgatcGATCgatc--GATCgatcBBBGATCgatcGATC-atcGATCBgatcGATCgatcGAT-CgatcGATgatcGATCgatcNNNNGATCFF..
# ZZFFFFgatcGATCgatcGATCgatc--GATCgatc........................................................................
# ...................AT-----------------BG-------GAT--------------------------------------------tcttttttt.....
my $pretty = $align->alignment;
print $pretty,"\n";
# dna1 1 ..FFFFgatc GATCgatcGA TCgatc--GA TCgatcG-B- ATCgatcGAT C-atcGATC- gatcGATCga tcGAT-Cgat
# dna2 1 ....FFgatc GATC----GA TCgatcNNGA TCgatcG--- ATCgatcGAT CgatcGATC- gatcGATC-- tcGATBCgat
# dna3 1 ..FFFFgatc GATCgatcGA TCgatc--GA TCgatcBBBG ATCgatcGAT C-atcGATCB gatcGATCga tcGAT-Cgat
# dna4 1 ZZFFFFgatc GATCgatcGA TCgatc--GA TCgatc.... .......... .......... .......... ..........
# dna5 1 .......... .........A T--------- ---------- -----BGGAT ---------- ---------- ----------
# dna1 72 cGATgatcGA TCgatcNNNN GATC....
# dna2 67 cGATCatcGA TCgatcNNNN GATCFFFF
# dna3 75 cGATgatcGA TCgatcNNNN GATCFF..
# dna4 35 .......... .......... ........
# dna5 8 ---------- ----tctttt ttt.....
DESCRIPTION
This is a utility module for pretty-printing the type of alignment that comes out of
gbrowse, namely a multiple alignment in which each target is aligned to a reference genome
without explicit pads or other spaces.
For speed and ease of use, the module does not use form Bio::SeqI objects, but raw strings
and alignment data structures. This may change.
This module does not perform multiple alignments! It merely pretty-prints them!
METHODS
This section describes the methods used by this class.
$aligner = Bio::Graphics::Browser2::PadAlignment->new(\@sequences,\@alignments)
Create a new aligner. The two arguments are \@sequences, an array ref to the list of
sequences to be aligned, and \@alignments, an array ref describing how the sequences
are to be aligned.
\@sequences should have the following structure:
[ name1 => $sequence1,
name2 => $sequence2,
name3 => $sequence3 ]
The sequences will be displayed in top to bottom order in the order provided. The
first sequence in the list is special because it is the reference sequence. All
alignments are relative to it.
\@alignments should have the following structure:
[ [ target1, $start1, $end1, $tstart1, $tend1 ],
[ target1, $start2, $end2, $tstart2, $tend2 ],
...
]
Each element of @alignments is an arrayref with five elements. The first element is
the name of the target sequence, which must be one of the named sequences given in
@sequences. The second and third elements are the start and stop position of the
aligned target segment relative to the reference sequence, "name1" in the example
given above. The fourth and fifth elements are the start and stop position of the
aligned target segment in the coordinate space of the target.
Example:
@dnas = ('dna1' => 'ccccccaaaaaatttt',
'dna2' => 'aaaaaa');
@alignment = ( ['dna2', 6, 11, 0, 5 ]);
Positions 0 to 5 of "dna2" align to positions 6-11 of "dna1".
Note that sequence positions are zero based. This may change.
@lines = $aligner->padded_sequences
This inserts pads into the sequences and returns them as a list of strings in the
order specified in new(). In a scalar context, this method will return a hashref in
which the keys are the sequence names and the values are their padded strings.
$map = $aligner->gap_map
This returns an arrayref indicating the position of each base in the gapped reference
sequence. The indexes are base positions, and the element values are their positions
in the reference sequence as returned by padded_sequences().
Note that the gap map only provides coordinate mapping for the reference sequence.
For an alternative implementation that provides gap maps for each of the targets (at
the cost of speed and memory efficiency) see the section after __END__ in the source
file for this module.
$align_string = $aligner->alignment(\%origins [,\%options])
This method returns a pretty-printed string of the aligned sequences. You may provide
a hashref of sequence origins in order to control the numbers printed next to each
line of the alignment. The keys of the %origins hashref are the names of the
sequences, and the values are the coordinate to be assigned to the first base of the
sequence. Use a negative number if you wish to indicate that the sequence has been
reverse complemented (the negative number should indicate the coordinate of the first
base in the provided sequence).
An optional second argument, if present, contains a hash reference to a set of
option=>value pairs. Three options are recognized:
show_mismatches 0|1 if true, highlight mismatches in pink
show_matches 0|1 if true, hightligt matches in yellow
color_code_proteins 0|1 if true, highlight amino acids thus:
Acidic amino acids in red
Basic amino acids in blue
Hydrophobic amino acids in grey
Polar amino acids in yellow
flip 0|1 if true, reverse complement the whole alignment
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Feature,
Bio::Graphics::FeatureFile, Bio::Graphics::Browser, Bio::Graphics::Browser2::Plugin
AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same
terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.