• NAME
• DESCRIPTION
• AUTHOR
• Overview
• Methods to read data into and output data from GFF objects.
• Methods to combine/manipulate GFF objects
• Methods to do calculations on GFF objects
• Misc methods.

NAME

DESCRIPTION

AUTHOR

Overview

Methods to read data into and output data from GFF objects.

read

Create GeneFeature object for each line of a stream from a GFF format file and add references to them to the GFF object

read_msp

Create HomolGeneFeature object for each line of a stream from an MSP file (output from MSPcrunch) and add references to them to the GFF object

dump

Dump out a GFF object (via method to dump out a GeneFeature object).

dump_pair

Dump out a GFF object (via method to dump out a GeneFeature object). Includes information about any pairing.

Methods to combine/manipulate GFF objects

addGeneFeature

Add a reference to a GeneFeature object to a GFF object

Methods to do calculations on GFF objects

Misc methods.

eachGeneFeature

Method to return an array of refs to the GeneFeatures in a GFF object

filter

Method to generate a new GFF object based on a filtered version of the object. Filtering is carried out by passing a reference to a subroutine, which is applied to each GeneFeature object.

count

Method to count the number of GeneFeature objects in a GFF object

self_overlap

Method to generate a new GFF object based on a filtered version of the object based on any pairwise overlap. Option to report overlaps to filehandle.

intersect_overlap

Method to generate a new GFF object based on intersection with second GFF object tolerance specifies error at each edge: tolerance=-1 specifies any overlap; tolerance=0 specifies exact match.

union

Method to generate a new GFF object which is a union of 2 GFF objects

member

Method to test if a GeneFeature object is a member of an existing GFF object (note - comparison is by reference only - does not check if 2 GeneFeature objects contain the same data!)

addGFF

Method to append GeneFeatures in a GFF object to another GFF object

cluster

Method to build an array of GFF objects each containing a group of GeneFeature objects sharing some attribute [pairwise comparison]

end_range

Method to find max range of members of a GFF object.

features

Method to return a hash of the cases and their occurance for a feature

group

Method to build an array of GFF objects each containing a group of GeneFeature objects sharing some attribute [fixed, named]

intersect_not

Method to generate a new GFF object which is everything in first GFF that is not in second GFF

intersect_overlap_pair

Method to generate a new GFFPair object based on intersection with second GFF object tolerance specifies error at each edge: tolerance=-1 specifies any overlap; tolerance=0 specifies exact match. single=1 specifies that only one edge needs to match tolerance strand=1 specifies that orientation must be identical

label

Method to add a label to each GeneFeature in this GFF point back to this GFF

label_pair

Method to make a list of the corresponding list of GFF's that the GeneFeatures in this GFF are paired with

maxScore

Method to find max score of members of a GFF object. If $paired, then only evaluates for objects which are lined to GFFPair object

maxScoreGf

Method to return GF object with max score in a GFF object.

max_min_range

Method to find max and min range of members of a GFF object.

shared_paired

Method to return a number of paired GeneFeature objects between 2 GFF's

start_range

Method to find min range of members of a GFF object.

strand

Method return strand of gf objects in gff

theFeature

Method to test if features returns a single value and return it