Free bio graphics feature 1.4 software for linux

Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel.

SYNOPSIS

use Bio::Graphics::Feature;

# create a simple feature with no internal structure
$f = Bio::Graphics::Feature->new(-start => 1000,
-stop => 2000,
-type => transcript,
-name => alpha-1 antitrypsin,
-desc => an enzyme inhibitor,
);

# create a feature composed of multiple segments, all of type "similarity"
$f = Bio::Graphics::Feature->new(-segments => [[1000,1100],[1500,1550],[1800,2000]],
-name => ABC-3,
-type => gapped_alignment,
-subtype => similarity);

# build up a gene exon by exon
$e1 = Bio::Graphics::Feature->new(-start=>1,-stop=>100,-type=>exon);
$e2 = Bio::Graphics::Feature->new(-start=>150,-stop=>200,-type=>exon);
$e3 = Bio::Graphics::Feature->new(-start=>300,-stop=>500,-type=>exon);
$f = Bio::Graphics::Feature->new(-segments=>[$e1,$e2,$e3],-type=>gene);

This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing.

Bio::DB::GFF::Feature is a relative segment identified by a feature type.

Bio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and its ancestors. It also inherits from Bio::SeqFeatureI and so has the familiar start(), stop(), primary_tag() and location() methods (it implements Bio::LocationI too, if needed).

Bio::DB::GFF::Feature adds new methods to retrieve the annotations type, group, and other GFF attributes. Annotation types are represented by Bio::DB::GFF::Typename objects, a simple class that has two methods called method() and source(). These correspond to the method and source fields of a GFF file.

Annotation groups serve the dual purpose of giving the annotation a human-readable name, and providing higher-order groupings of subfeatures into features. The groups returned by this module are objects of the Bio::DB::GFF::Featname class.

Bio::DB::GFF::Feature inherits from and implements the abstract methods of Bio::SeqFeatureI, allowing it to interoperate with other Bioperl modules.
Generally, you will not create or manipulate Bio::DB::GFF::Feature objects directly, but use those that are returned by the Bio::DB::GFF::RelSegment->features() method.
Important note about start() vs end()

If features are derived from segments that use relative addressing (which is the default), then start() will be less than end() if the feature is on the opposite strand from the reference sequence. This breaks Bio::SeqI compliance, but is necessary to avoid having the real genomic locations designated by start() and end() swap places when changing reference points.

To avoid this behavior, call $segment->absolute(1) before fetching features from it. This will force everything into absolute coordinates.

For example:

my $segment = $db->segment(CHROMOSOME_I);
$segment->absolute(1);
my @features = $segment->features(transcript);

Bio::Graphics::Glyph::minmax is the minmax glyph.

SYNOPSIS

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

This glyph is the common base class for Bio::Graphics::Glyph::graded_segments and Bio::Graphics::Glyph::xyplot. It adds an internal method named minmax() for calculating the upper and lower boundaries of scored features, and is not intended for end users.

Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects.

SYNOPSIS

# This script parses a GenBank or EMBL file named on the command
# line and produces a PNG rendering of it. Call it like this:
# render.pl my_file.embl | display -

use strict;
use Bio::Graphics;
use Bio::SeqIO;

my $file = shift or die "provide a sequence file as the argument";
my $io = Bio::SeqIO->new(-file=>$file) or die "could not create Bio::SeqIO";
my $seq = $io->next_seq or die "could not find a sequence in the file";

my @features = $seq->all_SeqFeatures;

# sort features by their primary tags
my %sorted_features;
for my $f (@features) {
my $tag = $f->primary_tag;
push @{$sorted_features{$tag}},$f;
}

my $panel = Bio::Graphics::Panel->new(
-length => $seq->length,
-key_style => between,
-width => 800,
-pad_left => 10,
-pad_right => 10,
);
$panel->add_track( arrow => Bio::SeqFeature::Generic->new(-start=>1,
-end=>$seq->length),
-bump => 0,
-double=>1,
-tick => 2);
$panel->add_track(generic => Bio::SeqFeature::Generic->new(-start=>1,
-end=>$seq->length),
-glyph => generic,
-bgcolor => blue,
-label => 1,
);

# general case
my @colors = qw(cyan orange blue purple green chartreuse magenta yellow aqua);
my $idx = 0;
for my $tag (sort keys %sorted_features) {
my $features = $sorted_features{$tag};
$panel->add_track($features,
-glyph => generic,
-bgcolor => $colors[$idx++ % @colors],
-fgcolor => black,
-font2color => red,
-key => "${tag}s",
-bump => +1,
-height => 8,
-label => 1,
-description => 1,
);
}

print $panel->png;
$panel->finished;

exit 0;

The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature and Das::Segment::Feature objects. It can be used to draw sequence annotations, physical (contig) maps, or any other type of map in which a set of discrete ranges need to be laid out on the number line.

The module supports a drawing style in which each type of feature occupies a discrete "track" that spans the width of the display. Each track will have its own distinctive "glyph", a configurable graphical representation of the feature.
The module also supports a more flexible style in which several different feature types and their associated glyphs can occupy the same track. The choice of glyph is under run-time control.

Semantic zooming (for instance, changing the type of glyph depending on the density of features) is supported by a callback system for configuration variables. The module has built-in support for Bio::Das stylesheets, and stylesheet-driven configuration can be intermixed with semantic zooming, if desired.

You can add a key to the generated image using either of two key styles. One style places the key captions at the top of each track. The other style generates a graphical key at the bottom of the image.

Note that this module depends on GD. The optional SVG output depends on GD::SVG and SVG.

Bio::Seq is a sequence object, with features.

SYNOPSIS

# This is the main sequence object in Bioperl

# gets a sequence from a file
$seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat);
$seqobj = $seqio->next_seq();

# SeqIO can both read and write sequences; see Bio::SeqIO
# for more information and examples

# get from database
$db = Bio::DB::GenBank->new();
$seqobj = $db->get_Seq_by_acc(X78121);

# make from strings in script
$seqobj = Bio::Seq->new( -display_id => my_id,
-seq => $sequence_as_string);

# gets sequence as a string from sequence object
$seqstr = $seqobj->seq(); # actual sequence as a string
$seqstr = $seqobj->subseq(10,50); # slice in biological coordinates

# retrieves information from the sequence
# features must implement Bio::SeqFeatureI interface

@features = $seqobj->get_SeqFeatures(); # just top level
foreach my $feat ( @features ) {
print "Feature ",$feat->primary_tag," starts ",$feat->start," ends ",
$feat->end," strand ",$feat->strand,"n";

# features retain link to underlying sequence object
print "Feature sequence is ",$feat->seq->seq(),"n"
}

# sequences may have a species

if( defined $seq->species ) {
print "Sequence is from ",$species->binomial_name," [",$species->common_name,"]n";
}

# annotation objects are Bio::AnnotationCollectionIs
$ann = $seqobj->annotation(); # annotation object

# references is one type of annotations to get. Also get
# comment and dblink. Look at Bio::AnnotationCollection for
# more information

foreach my $ref ( $ann->get_Annotations(reference) ) {
print "Reference ",$ref->title,"n";
}

# you can get truncations, translations and reverse complements, these
# all give back Bio::Seq objects themselves, though currently with no
# features transfered

my $trunc = $seqobj->trunc(100,200);
my $rev = $seqobj->revcom();

# there are many options to translate - check out the docs
my $trans = $seqobj->translate();

# these functions can be chained together

my $trans_trunc_rev = $seqobj->trunc(100,200)->revcom->translate();

A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface.

In Bioperl we have 3 main players that people are going to use frequently

Bio::PrimarySeq - just the sequence and its names, nothing else.
Bio::SeqFeatureI - a location on a sequence, potentially with a sequence
and annotation.
Bio::Seq - A sequence and a collection of sequence features
(an aggregate) with its own annotation.

Although Bioperl is not tied heavily to file formats these distinctions do map to file formats sensibly and for some bioinformaticians this might help

Bio::PrimarySeq - Fasta file of a sequence
Bio::SeqFeatureI - A single entry in an EMBL/GenBank/DDBJ feature table
Bio::Seq - A single EMBL/GenBank/DDBJ entry

By having this split we avoid a lot of nasty circular references (sequence features can hold a reference to a sequence without the sequence holding a reference to the sequence feature). See Bio::PrimarySeq and Bio::SeqFeatureI for more information.

Ian Korf really helped in the design of the Seq and SeqFeature system.

Bio::Graph::SimpleGraph is a Perl module that can create and manipulate undirected graphs.

SYNOPSIS

use Bio::Graph::SimpleGraph;

my $graph=new SimpleGraph;
# read pairs of nodes from STDIN
while () {
my($node1,$node2)=split;
$graph->add_edge($node1,$node2);
}
my @nodes=graph->nodes; # get list of nodes
my @edges=graph->edges; # get list of edges
foreach my $node (@nodes) {
my @neighbors=$node->neighbors; # get list of neighboring nodes
}

This is a simple, hopefully fast undirected graph package. The only reason this exists is that the standard CPAN Graph pacakge, Graph::Base, is seriously broken. The package implements a small and eclectic assortment of standard graph algorithms that we happened to need for our applications.

This module is a subclass of Class::AutoClass (available at CPAN). AutoClass auotgenerates simple accessor and mutator methods (aka get and set methods). It also automates class initialization.

Nodes can be any Perl values, including object references. Edges are pairs of nodes.

(Caveat: be careful with values that contain embedded instances of $; (the character Perl uses to separate components of multi-dimensional subscripts), because we use this in the text representation of edges.

The main data structures are:

An edge (x,y) is represented canonically as a two element list in
which the lexically smaller value is first. Eg, the node (b,a)
is represented as [a,b].

The graph contains

1) A hash mapping the text representation of a node to the node
itself. This is mostly relevant when the node is a reference.

2) A hash mapping the text representation of a node to a list of
the nodes neighbors.

3) A hash mapping the text representation of an edge to the edge itself.

Bio::SeqIO::fastq is a fastq sequence input/output stream.

SYNOPSIS

Do not use this module directly. Use it via the Bio::SeqIO class.

This object can transform Bio::Seq and Bio::Seq::SeqWithQuality objects to and from fastq flat file databases.

Fastq is a file format used frequently at the Sanger Centre to bundle a fasta sequence and its quality data. A typical fastaq entry takes the from:

@HCDPQ1D0501
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT.....
+HCDPQ1D0501
!*((((***+))%%%++)(%%%%).1***-+*))**55CCF>>>>>>CCCCCCC65.....

Fastq files have sequence and quality data on a single line and the quality values are single-byte encoded. To retrieve the decimal values for qualities you need to subtract 33 (or Octal 41) from each byte and then convert to a 2 digit + 1 space integer. You can check if 33 is the right number because the first byte which is always ! corresponds to a quality value of 0.

Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s).

SYNOPSIS

use strict;
use Bio::Index::Blast;
my ($indexfile,$file1, $file2);
my $index = new Bio::Index::Blast(-filename => $indexfile,
-write_flag => 1);
$index->make_index($file1, $file2);

my $id;
my $data = $index->get_stream($id);

my $bplite_report = $index->fetch_report($id);
print "query is ", $bplite_report->query, "n";
while( my $sbjct = $bplite_report->nextSbjct ) {
print $sbjct->name, "n";
while( my $hsp = $sbjct->nextHSP ) {
print "t e-value ", $hsp->P,
}
print "n";
}

This object allows one to build an index on a blast file (or files) and provide quick access to the blast report for that accession. Note: for best results use strict.