GFF::HomolGeneFeature - Perl extension for GFF Homology Gene Features
use GFF ; # performs an implicit 'use GFF::HomolGeneFeature;'
Copyright (c) 1999 Created by Tim Hubbard th@sanger.ac.uk.
Augmented by Richard Bruskiewich rbsk@sanger.ac.uk
Sanger Institute, Wellcome Trust Genome Campus, Cambs, UK All rights reserved.
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation.
GFF::HomolGeneFeature (derived from GFF) is a class of Perl object, derived
(subclassed) from the GFF::GeneFeature object class, that encapsulates a
single ``homology'' gene feature record (``line'') in the General Feature Format (``GFF'').
A GFF::GeneFeatureSet Perl object is the
container object for a set of GFF::HomolGeneFeature objects. One can now graphically
represent GFF::HomolGeneFeature objects as 'P' layout objects in the
GFF::GifGFF module.
How to Read Method Protocols
Normal Perl data type notations are used for argument declarations in the
method protocols. A backslash denotes argument passing by reference.
Class methods are invoked using the 'class->method(args)' or 'method
class args' Perl call formats.
The most current release of the Perl source code for this module is
available here.
All bug reports may be submitted to Richard Bruskiewich
(rbsk@sanger.ac.uk).
For all construction methods, an optional ``$version'' argument may be
given which sets the created object to a specified GFF specification
version. If this argument is not given, then the GFF class (package)
default version is used (see GFF->version()).
- new( $version )
-
Class method to construct a new, empty GFF::HomolGeneFeature object.
- new_from_line( $line, $version )
-
Class method to parse a ``homology'' gene feature
$line string
into a GFF::HomolGeneFeature object (creates and returns the object
reference).
- new_from_msp( $line, $source, \$name_parse, $version )
-
Class method to parse a line into a GFF::HomolGeneFeature from MSPcrunch
format (creates and returns the object reference). The
$source
string argument is used to fill the GFF source field with a tag name. The
optional &name_parser argument is user-defined function which
takes two arguments $group and \@array, where
@array is assumed to be the (delimiter split) remainder of a
line of data beyond the group field.
- new_from_parse( $line, \&parser, $version )
-
Class method to parse the
$line string into the
GFF::HomolGeneFeature object using a user defined &parser
function (creates and returns the object reference). The
&parser should expect the (empty) GFF::HomolGeneFeature object
reference as its first argument and the input line (string) as its second
argument. So given, the function should perform the appropriate parsing of
the input $line to load the GFF::HomolGeneFeature object with
data.
- copy( $version )
-
Method to duplicate the invoking GFF::HomolGeneFeature object.
- fromGeneFeature( $version (See below for other arguments) )
-
A ``type cast'' method to convert an GeneFeature object into a
GFF::HomolGeneFeature object.
- Version 1 GFF protocol
-
fromGeneFeature( 1, $target, $start2, $end2 )
where he $target string is the [group] field
name of the homologous sequence. The start coordinate of the match
(``$start2'') and end coordinate of the match (``$end2'') should also be
given.
- Version 2 GFF protocol or better
-
fromGeneFeature( 2, $group ) where if the (optional)
$group string argument is given, it is
parsed as a string containing a Version 2 style semicolon delimited
tag-value pair [group] field description of the homology match. The
recommended Version 2 format for such group fields is described in the GFF
homology feature specification. If the $group argument is
omitted or null, then the group() hash from the GeneFeature
object is dereferenced for 'Target' and 'E_value' tags with associated
GFF::HomolGeneFeature specific values.
- dump( \*OUTPUT, $tab, $flen )
-
Method uses
dump_string() to write a formatted output of a
GeneFeature object to a filehandle, OUTPUT. If \*OUTPUT is not given,
\*STDOUT is used. The ``$tab'' argument is a boolean flag, where a non-null
value directs the use tab as the field delimiter in the output line;
otherwise, use blank space (flag is assumed null if not specified). The
``$flen'' argument is a boolean flag, where a non-null value stipulates
that the length of the current output line should be printed as an extra
field at the end of the output line (assumed null if not specified. Note:
the extra length of this field is *not* added to the displayed line size,
but the extra field is tab delimited, if $tab is set).
- dump_string( $tab )
-
Method to return a formatted output of a GFF::HomolGeneFeature object to a
string. The optional ``$tab'' argument is a boolean flag, where a non-null
value directs the use tab as the field delimiter in the output line;
otherwise, use blank space (flag is assumed null if not specified).
The various GFF record fields may be set or queried by (inherited)
GeneFeature access methods. Additional GFF::HomolGeneFeature fields are
available by the following access methods. All the methods can take a
single string argument to set the variable. With or without an argument,
the methods return the current (or newly set) value, as a string, except as
specifically noted below:
- target()
-
(Version 2) homology target (is simply [group] name in Version 1 GFF).
- start2()
-
start coordinate of the homologous match sequence.
- end2()
-
end coordinate of the homologous match sequence.
- percentid()
-
percentage identity between query and match sequence.
- exp_value()
-
(Version 2) expectation value.
- gap( $HGF2, $warn )
-
Method to determine the gap between the invoking and a second (``$HGF2'')
GFF::HomolGeneFeature object. Note: The method assumes that the invoking
GFF::HomolGeneFeature object lies upstream (to the left of) the other
object. If the optional ``$warn'' flag is defined and set to non-null, then
the method prints additional warning diagnostics onto STDOUT, e.g. possible
frameshifts and indel's between the two GFF::HomolGeneFeature objects.
Returns a reference to a newly created GFF::HomolGeneFeature object
representing the gap.
4/5/99 - rbsk: renamed HomolGeneFeature.pm =>
GFF::HomolGeneFeature.pm
3/3/99 - rbsk:
extensively revised and improved the
documentation added Version 2 GFF code,
especially group() field management methods
GFF, GFF::GeneFeature,
GFF::GeneFeatureSet,
GFF::Analysis, GFF::GifGFF.