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.