GVF-Parser

A Lite parser for Genome Variation Format (GVF) files.  


GVF BACKGROUND

The Genome Variation Format (GVF) is a very simple file format for describing sequence_alteration features at nucleotide resolution relative to a reference genome. The GVF format was published in Reese et al., Genome Biol., 2010;11(8):R88

GVF is a type of GFF3 file with additional pragmas and attributes specified. The GVF format has the same nine-column tab-delimited format as GFF3. All of the requirements and restrictions specified for GFF3 apply to the GVF specification as well and thus a GVF file should be fully compatible with code used for processing and displaying GFF3 files. In addition, GVF adds additional constraints to some of these columns as described via http://www.sequenceontology.org/resources/gvf.html


GVF::Parser

GVF::Parser partitions GVF files into pragma and feature data, and the feature data is further split into features and attributes.  Pragma data is stored in object, and can be requested using the pragmaRequest method.  Attribute information is stored/saved in a sqlite datafile, and can be accessed using the attributeRequest method, or more preferably via DBIx::Class requestset.  


INSTALLATION

To install this module, run the following commands:

	perl Makefile.PL
	make
	make test
	make install

SUPPORT AND DOCUMENTATION

After installing, you can find documentation for this module with the
perldoc command.

    perldoc GVF::Parser

You can also look for information at:

    RT, CPAN's request tracker (report bugs here)
        http://rt.cpan.org/NoAuth/Bugs.html?Dist=GVF-Parser

    AnnoCPAN, Annotated CPAN documentation
        http://annocpan.org/dist/GVF-Parser

    CPAN Ratings
        http://cpanratings.perl.org/d/GVF-Parser

    Search CPAN
        http://search.cpan.org/dist/GVF-Parser/


LICENSE AND COPYRIGHT

Copyright (C) 2012 Shawn Rynearson

This program is free software; you can redistribute it and/or modify it
under the terms of either: the GNU General Public License as published
by the Free Software Foundation; or the Artistic License.

See http://dev.perl.org/licenses/ for more information.

