Ubuntu Manpage: Bio::Graphics::Glyph::segments

Provided by: libbio-graphics-perl_2.40-2_all

NAME

       Bio::Graphics::Glyph::segments - The "segments" glyph

SYNOPSIS

         See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION

This glyph is used for drawing features that consist of discontinuous segments. Unlike
"graded_segments" or "alignment", the segments are a uniform color and not dependent on
the score of the segment.

METHODS
This module overrides the maxdepth() method to return 1 unless explicitly specified by the
-maxdepth option. This means that modules inheriting from segments will only be presented
with one level of subfeatures. Override the maxdepth() method to get more levels.

OPTIONS
The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full
explanation.

Option Description Default
------ ----------- -------

-fgcolor Foreground color black

-outlinecolor Synonym for -fgcolor

-bgcolor Background color turquoise

-fillcolor Synonym for -bgcolor

-linewidth Line width 1

-height Height of glyph 10

-font Glyph font gdSmallFont

-connector Connector type 0 (false)

-connector_color
Connector color black

-label Whether to draw a label 0 (false)

-description Whether to draw a description 0 (false)

-strand_arrow Whether to indicate 0 (false)
strandedness

-hilite Highlight color undef (no color)

In addition, the following glyph-specific options are recognized:

-draw_dna If true, draw the dna residues 0 (false)
when magnification level
allows.

-draw_target If true, draw the dna residues 0 (false)
of the TARGET sequence when
magnification level allows.
See "Displaying Alignments".

-draw_protein_target If true, draw the protein residues 0 (false)
of the TARGET sequence when
magnification level allows.
See "Displaying Alignments".

-ragged_extra When combined with -draw_target, 0 (false)
draw extra bases beyond the end
of the alignment. The value is
the maximum number of extra
bases.
See "Displaying Alignments".

-ragged_start Deprecated option. Use
-ragged_extra instead

-show_mismatch When combined with -draw_target, 0 (false)
highlights mismatched bases in
the mismatch color.
Can be 0 (don't display);
1 (display when the DNA fits);
or another positive integer
(display when the region in
view is <= this value).
See "Displaying Alignments".

-mismatch_only When combined with -draw_target, 0 (false)
draws only the mismatched bases
in the alignment. Implies
-show_mismatch.
See "Displaying Alignments".

-mismatch_color The mismatch color to use 'lightgrey'

-insertion_color The color to use for insertions 'green'
relative to the reference.

-deletion_color The color to use for deletions 'red'
relative to the reference.

-indel_color The color to use for indels, used 'lightgrey'
only if -insertion_color or
-deletion_color are absent

-true_target Show the target DNA in its native 0 (false)
(plus strand) orientation, even if
the alignment is to the minus strand.
See "Displaying Alignments".

-realign Attempt to realign sequences at 0 (false)
high mag to account for indels.
See "Displaying Alignments".

If the -draw_dna flag is set to a true value, then when the magnification is high enough,
the underlying DNA sequence will be shown. This option is mutually exclusive with
-draw_target. See Bio::Graphics::Glyph::generic for more details.

The -draw_target, -ragged_extra, and -show_mismatch options only work with seqfeatures
that implement the hit() method (Bio::SeqFeature::SimilarityPair). -draw_target will cause
the DNA of the hit sequence to be displayed when the magnification is high enough to allow
individual bases to be drawn. The -ragged_extra option will cause the alignment to be
extended at the extreme ends by the indicated number of bases, and is useful for looking
for polyAs and cloning sites at the ends of ESTs and cDNAs. -show_mismatch will cause
mismatched bases to be highlighted in with the color indicated by -mismatch_color. A
-show_mismatch value of "1" will highlight mismatches only when the base pairs are
displayed. A positive integer will cause mismatches to be shown whenever the region in
view is less than or equal to the requested value.

At high magnifications, minus strand matches will automatically be shown as their reverse
complement (so that the match has the same sequence as the plus strand of the source dna).
If you prefer to see the actual sequence of the target as it appears on the minus strand,
then set -true_target to true.

Note that -true_target has the opposite meaning from -canonical_strand, which is used in
conjunction with -draw_dna to draw minus strand features as if they appear on the plus
strand.

Displaying Alignments
When the -draw_target option is true, this glyph can be used to display nucleotide
alignments such as BLAST, FASTA or BLAT similarities. At high magnification, this glyph
will attempt to show how the sequence of the source (query) DNA matches the sequence of
the target (the hit). For this to work, the feature must implement the hit() method, and
both the source and the target DNA must be available. If you pass the glyph a series of
Bio::SeqFeature::SimilarityPair objects, then these criteria will be satisified.

Without additional help, this glyph cannot display gapped alignments correctly. To
display gapped alignments, you can use the Bio::Graphics::Brower::Realign module, which is
part of the Generic Genome Browser package (http://www.gmod.org). If you wish to install
the Realign module and not the rest of the package, here is the recipe:

cd Generic-Genome-Browser-1.XX
perl Makefile.PL DO_XS=1
make
make install_site

If possible, build the gbrowse package with the DO_XS=1 option. This compiles a C-based
DP algorithm that both gbrowse and gbrowse_details will use if they can. If DO_XS is not
set, then the scripts will use a Perl-based version of the algorithm that is 10-100 times
slower.

The display of alignments can be tweaked using the -ragged_extra, -show_mismatch,
-true_target, and -realign options. See the options section for further details.

There is also a -draw_protein_target option, which is designed for protein to nucleotide
alignments. It draws the target sequence every third base pair and is supposed to align
correctly with the forward and reverse translation glyphs. This option is experimental at
the moment, and may not work correctly, to use with care.

BUGS

       Please report them.

AUTHOR

       Lincoln Stein <lstein@cshl.org>

       Copyright (c) 2001 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.

NAME

SYNOPSIS

DESCRIPTION

BUGS

SEE ALSO

AUTHOR